structural basis for broad and potent neutralization of hiv-1 by antibody vrc01

8/8/2019 Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01

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During HIV-1 infection, antibodies are generated against

the region of the viral gp120 envelope glycoprotein that

binds CD4, the primary receptor for HIV-1. Among these

antibodies, VRC01 achieves broad neutralization of

diverse viral strains. Here we determine the crystal

others have screened cohorts of sera from infectto find broadly neutralizing responses that are desubstantial percentage of subjects (6-10). One sethat satisfies these criteria has been mapped to thHIV-1 gp120 envelope (Env) glycoprotein that b

Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VTongqingZhou,1IvelinGeorgiev,1*XuelingWu,1*Zhi-YongYang,1*KaifanDai,1AndrsFinzDo Kwon,1JohannesScheid,3WeiShi,1LingXu,1YongpingYang,1JiangZhu,1Michel C.NusseJosephSodroski,2,4LawrenceShapiro,1,5Gary J.Nabel,1John R.Mascola,1Peter D.Kwong11Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth20892, USA. 2Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Patholoof AIDS, Harvard Medical School, Boston, MA 02115, USA. 3Laboratory of Molecular Immunology and Howard

Medical Institute, The Rockefeller University, New York, New York 10065 USA.4

Department of Immunology anDiseases, Harvard School of Public Health, Boston, MA 02115, USA. 5Department of Biochemistry and MolecularColumbia University, New York, NY 10032, USA.

*These authors contributed equally to this work.

To whom correspondence should be addressed. E-mail: [email protected]


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orthorhombic crystals, which contained four copies of theVRC01-gp120 complex per asymmetric unit, and thestructure was solved by molecular replacement and refined toan R-value of 19.7% (Rfree of 25.6%) (Fig. 1 and table S1)

(15).The interaction surface between VRC01 and gp120

encompasses almost 2500 2, 1244 2 contributed by VRC01and 1249 2by gp120 (16). On VRC01, both heavy chain(894 2) and light chain (351 2) contribute to the contactsurface (table S2), with the central focus of binding on theheavy chain-second complementarity-determining region(CDR H2). Over half of the interaction surface of VRC01

(644 2

) involves CDR H2, a mode of binding reminiscent ofthe interaction between gp120 and the CD4 receptor; CD4 isa member of the V-domain class of the immunoglobulinsuperfamily (17), and the CDR2-like region of CD4 is acentral focus of gp120 binding (Figs. 2A and table S3) (18).For CD4, the CDR2-like region forms antiparallel,intermolecular hydrogen-bonds with residues 365-368gp120 ofthe CD4-binding loop of gp120 (18) (Fig. 2B); with VRC01,one hydrogen-bond is observed between the carbonyl ofGly54VRC01 and the backbone nitrogen of Asp368gp120. Thishydrogen-bond occurs at the loop tip, an extra residue relativeto CD4 is inserted in the strand, and the rest of the potential

gp120, though with considerable variation. Anaelectrostatics shows that the interaction surfacesand CD4 are both quite basic, though the residucontacting amino acids are distinct (fig. S2). Thu

VRC01 mimics CD4 binding to some extent, codifferences are observed.

Structural basis of VRC01 breadth and po

CD4 is placed into an immunoglobulin context btwo N-terminal domains to a dimeric immunoglconstant region, it achieves reasonable neutralizVRC01, however, neutralizes better (Fig. 3A) (1understand the structural basis for the exception

potency of VRC01, we analyzed its interactive sgp120. VRC01 focuses its binding onto the confinvariant outer domain, which accounts for 87%contact-surface area of VRC01 (table S7). The 1contacts made with flexible inner domain and brare non-contiguous and are not critical for bindicontrast, CD4 makes 33% of its contacts with thsheet, and many of these interactions are essentireduction in inner domain and bridging sheet intVRC01 is accomplished primarily by a 6- tranrelative to CD4, away from these regions; criticasuch as made by Phe43CD4 to the nexus of the br


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that hinders most CD4-binding-site ligands (25) and toneutralize HIV-1 potently (26).

Precise targeting by VRC01. Prior analysis of effectiveand ineffective CD4-binding-site antibodies suggested that

precise targeting to the vulnerable site of initial CD4attachment is required to block viral entry (11, 27). This siterepresents the outer domain-contact site for CD4 (22).Analysis of the VRC01 interaction with gp120 shows that itcovers 98% of this site (Figs. 4A, 4B and fig. S4), comprising1089 2 on the gp120 outer domain, about 50% larger thanthe 730 2 surface covered by CD4. The VRC01 contactsurface outside the target site is largely limited to the

conformationally invariant outer domain and avoids regionsof conformational flexibility. This concordance of binding ismuch greater than for ineffective CD4-binding-siteantibodies, as well as for those that are partially effective,such as antibody b12 (11, 22) (fig. S4).

The outer domain-contact site for CD4 is shielded byglycan (22). Contacts by the VRC01 light chain (Tyr28VRC01and Ser30VRC01) are made with the protein-proximal N-acetyl-glucosamine from the N-linked glycan at residue 276gp120(28). Thus, instead of being occluded by glycan, VRC01makes use of a glycan for binding. Other potential glycaninteractions may occur with different strains of HIV-1 gp120,

more conserved residues at the loop base, VRC0variation in the tip of the V5 loop (Fig. 4D).

Unusual VRC01 features and contribution

recognition. We examined the structure of VRC

special features that might be required for its funnumber of unusual features were apparent, includegree of affinity maturation, an extra disulfide for N-linked glycosylation, a 2-amino acid deletlight chain, and an extensively matured binding

between VRC01 and gp120 (Fig. 5 and fig. S9).the frequency with which these features were foEnv-reactive antibodies (SOM Appendix) or in

antibody-antigen complexes (fig. S10 and tablesmeasured the effect of genomic reversion of theaffinity for gp120 and neutralization of virus (Fitable S10).

Higher levels of affinity maturation have beeHIV-1 reactive antibodies in general (29), and mhigher levels for broadly neutralizing ones (30).maturation levels could be a by-product of the pnature of HIV-1 infection, and may not represenrequirement. Removal of the N-linked glycosylaextra disulfide bond, which connects CDR H1 aof the heavy chain, had little effect on binding o


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with elements encoded in single genomic elements orcassettes, suggesting that specific joints between them are notrequired. Within the VH cassette, a number of residuesassociated with the IGHV1-02*02 precursor of VRC01

interact with gp120; many of these are conserved in relatedgenomic VHs, some of which are of similar genetic distancefrom VRC01 (fig. S12). These results suggest that appropriategenomic precursors for VRC01 are likely to occur at areasonable frequency in the human antibody repertoire.

Recombination produces nascent B cell-presentedantibodies that have reactivities against both self and nonselfantigens. Those with auto-reactivity are removed through

clonal deletion. With many of the broadly neutralizing anti-HIV-1 antibodies, such as 2G12 (glycan reactive) (32-33),2F5 and 4E10 (membrane reactive) (34-35), this appears to bea major barrier to elicitation. While this remains to becharacterized for genomic revertants and intermediates, noauto-reactivity has so far been observed with VRC01 (12).

The third step influencing the elicitation of VRC01-likeantibodies is affinity maturation, a process involvinghypermutation of variable domains combined with affinity-

based selection that occurs during B cell maturation ingerminal centers (36). In the case of VRC01, 41 residuealterations were observed from the genomic VH-gene and 25

rather than focused on the VRC01-gp120 interfacontact residues therefore appear to influence thwith gp120 through indirect protein-folding effeVRC01, the process of affinity maturation entai

changes of the nascent genomic precursors to obaffinity interaction with HIV-1 Env surface.

Receptor mimicry and affinity maturation

possibility of antibodies using conserved sites ofrecognition to neutralize viruses effectively has for several decades. The recessed canyon on rhirecognizes the unpaired terminal immunoglobulICAM-1 highlights the steric role that a narrow

entrance may play in occluding bivalent antibodregions (39), although framework recognition cainstances permit entry (40). Partial solutions suc

presented by antibody b12 (neutralization of 40%circulating isolates) (22) or by antibody HJ16 (nof 30% of circulating isolates) (41), a recently idCD4-binding-site antibody, may allow recognitiHIV-1 isolates.

With VRC01, the potency and breadth of neu(over 90%) suggests a more general solution. It seen how difficult it will be to guide the elicitatiVRC01-like antibodies from genomic rearrange


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12. X. Wu et al., Science, published online 8 July 2010(10.1126/science.1187659).

13. The Env components of this strain derive from Clade EHIV-1 lineages (42).

14. M. Pancera et al., Proc Natl Acad Sci U S A107, 1166(2010).

15. The four independent copies of the VRC01-gp120complex in the asymmetric unit resembled each otherclosely for the antibody variable domain-gp120components, with an C-root-mean-square deviation ofless than 0.2 . Elbow variation, however, betweenvariable and constant domains was apparent, and we found

one copy (molecule 1) to be more ordered than the others.In figures, we display molecule 1; see Fig. S15 for acomparison of all of the molecules in the asymmetric unit.

16. Surface areas of interaction reported in this paper weredetermined with the program PISA, as implemented inCCP4 (43). Values were about 20% higher than thosereported previously for the gp120-CD4 complex (18),which were obtained using the program MS (44).

17. P. J. Maddon et al., Cell42, 93 (1985).18. P. D. Kwong et al.,Nature393, 648 (1998).19. The overlap of molecular volumes was calculated by

comparing the separate volumes of interacting domains

interactions with the N-acetyl-glycosamine a276gp120 shows that both 1,4 additions and 1,6tolerated.

29. J. F. Scheid et al.,Nature458, 636 (2009).

30. C. C. Huang et al., Proc Natl Acad Sci U S A(2004).

31. Four residues are provided by the CDR H3, Trp100BVRC01, with a combined interaction su2 (tables S3 and S12). These four residues acontributed by the D segment (IGHD3-16*02of them appears critical to VRC01 recognitioare observed in two of these residues in the c

broadly-neutralizing antibody VRC03, whichtwo antibodies we isolated along with VRC0Meanwhile, three residues are provided by thTyr91VRC01, Glu96VRC01 and Phe97VRC01, withinteraction surface of 190 2 (tables S3 and Sthree residues lie at the junction between V- They make important hydrophobic interactioD of gp120, and two of them are conserved bVRC01 and VRC03. While it is difficult to k

precisely the CDR L3 needs to be aligned, wcontact residues, variation at the VK-J gene juprovide sufficient diversity for it to be repres


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mature, then maturation would either not occur or wouldneed to occur in response to a different immunogen. Thislack of guided initiation of the maturation process may

provide an explanation for the absence of such broadly

neutralizing antibodies in the first few years of infection.Conversely, the introduction of modified gp120s withaffinity to genomic precursors and affinity maturationintermediates could provide a mechanism by which toelicit antibodies like VRC01.

39. M. G. Rossmann,J Biol Chem264, 14587 (1989).40. T. J. Smith, E. S. Chase, T. J. Schmidt, N. H. Olson, T. S.

Baker,Nature383, 350 (1996).

41. D. Corti et al., PLoS ONE5, e8805 (2010).42. J. P. Anderson et al.,J Virol74, 10752 (2000).43. Collaborative Computational Project,Acta Crystallogr D

Biol Crystallogr50, 760 (1994).44. M. L. Connolly,J Mol Graph11, 139 (1993).45. D. G. Myszka et al., Proc Natl Acad Sci U S A97, 9026

(2000).46. X. Xiao, W. Chen, Y. Feng, D. S. Dimitrov, Viruses1,

802 (2009).

47. X. Xiao et al.,Biochem Biophys Res Commun390, 404(2009).

48. M. Pancera et al., J Virol, (2010).

Figures S1 to S16Tables S1 to S14ReferencesAppendix S1

25 May 2010; accepted 1 July 2010Published online 8 July 2010; 10.1126/science.1Include this information when citing this paper.

Fig. 1. Structure of antibody VRC01 in complexgp120. Atomic-level details for broad and potenof HIV-1 by a natural human antibody are depic

polypeptide chains in ribbon representations. Th

domain is shown in gray, the bridging sheet in bouter domain in red, except for the CD4-binding(purple), the D loop (brown), and the V5 loop (olight chain of the antigen-binding fragment (Fabis shown in light blue with complementarity-detregions (CDRs) highlighted in dark blue (CDR Lmarine blue (CDR L3). The heavy chain of Fab shown in light green with CDRs highlighted in c

H1), green (CDR H2), and pale yellow (CDR Hand heavy chains of VRC01 interact with gp120interaction surface is provided by the CDR H2, w


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Polypeptides are shown in ribbon representation, with gp120colored the same as in A and VRC01 depicted with heavychain in dark yellow and light chain in dark gray. When theheavy chain of VRC01 is superimposed onto CD4 in the

CD4-gp120 complex, the position assumed by the light chainevinces numerous clashes with gp120 (left). The VRC01-

binding orientation (right) avoids clashes by adopting anorientation rotated by 43 and translated by 6-.

Fig. 3. Structural basis of antibody VRC01 neutralizationbreadth and potency.VRC01 displays remarkableneutralization breadth and potency, a consequence in part ofits ability to bind well to different conformations of HIV-1

gp120. (A) Neutralization dendrograms. The genetic diversityof current circulating HIV-1 strains is displayed as adendrogram, with locations of prominent clades (e.g. A, Band C) and recombinants (e.g. CDR02_AG) labeled. Thestrains are colored by their neutralization sensitivity toVRC01 (left) or CD4 (right). VRC01 neutralizes 72% of thetested HIV-1 isolates with an IC80 of less than 1 ug/ml; bycontrast, CD4 neutralizes 30% of the tested HIV-1 isolates

with an IC80 of less than 1 ug/ml (table S14). (B) Comparisonof binding affinities. Binding affinities (KDs) for VRC01 andvarious other gp120-reactive ligands as determined by

f l h b h hi

the view in Figs. 1 and 2. (B) VRC01 recognitiomolecular surface of gp120 in the VRC01 boundconformation is colored as in A. The variable doVRC01 are shown in ribbon representation with

and light chains colored as in Fig. 1 and extensioregions indicated. (C) Antigenic variation. The p

backbone of gp120 is colored according to sequconservation, blue if conservation is high and reconservation is low. (D) Molecular surface of Vselect interactive loops of gp120. Variation at thV5 loop is accommodated by a gap between heachains of VRC01.

Fig. 5. Unusual VRC01 features.The structure odisplays a number of unusual features, which if recognition might inhibit the elicitation of VRCantibodies. In A-D, unusual features of VRC01 structurally (far left panel), in terms of frequenchistogram with other antibodies (second panel frin the context of affinity and neutralization meaafter mutational alteration (right two panels). Af

measurements were made by ELISA to the gp12used in crystallization (93TH057), and neutralizmeasurements were made with a clade A HIV-1Q842 d12 Addi i l bi di d li i


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affinity too low to measure to a tight (nM) interaction. (A)Effect of genomic reversions. The VH- and V-derivedregions of VRC01 were reverted to the sequences of theirclosest genomic precursors, expressed as immunoglobulins

and tested for binding as VH- and V-revertants (gHgL), as aVH-only revertant (gH), or as a V-only revertant (gL) to thegp120 construct used in crystallization (93TH057) or to astabilized HXBc2 core (22). These constructs were also testedfor neutralization of a clade A HIV-1 strain Q842.d12.Additional neutralization experiments with clade B and Cviruses are reported in the supplemental materials. (B)Maturation of VRC01 and correlation with binding and

neutralization. Affinity and neutralization measurements forthe 19 VRC01 mutants created during the structure-functionanalysis of VRC were analyzed in the context of their degreeof affinity maturation. Significant correlations were observed,with extrapolation to VH- and V-genomic revertantssuggesting greatly reduced affinity for gp120.


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structural basis for broad and potent neutralization of hiv-1 by antibody vrc01

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