7Z3A

AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein.

van Schooten, J.Farokhi, E.Schorcht, A.van den Kerkhof, T.L.G.M.Gao, H.van der Woude, P.Burger, J.A.Meesters, T.G.R.Bijl, T.Ghalaiyini, R.Turner, H.L.Dorning, J.van Schaik, B.D.C.van Kampen, A.H.C.Labranche, C.C.Stanfield, R.L.Sok, D.Montefiori, D.C.Burton, D.R.Seaman, M.S.Ozorowski, G.Wilson, I.A.Sanders, R.W.Ward, A.B.van Gils, M.J.

(2022) Nat Commun 13: 4515-4515

  • DOI: 10.1038/s41467-022-32208-0
  • Primary Citation of Related Structures:  
    7U04, 7U0K, 7Z3A, 7ZLK

  • PubMed Abstract: 
  • A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3) ...

    A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3). Here, we describe three IOMA-class NAbs, ACS101-103, with up to 37% breadth, that share many characteristics with IOMA, including an average-length CDRL3. Cryo-electron microscopy revealed that ACS101 shares interactions with those observed with other VH1-2 and VH1-46-class bNAbs, but exhibits a unique binding mode to residues in loop D. Analysis of longitudinal sequences from the patient suggests that a transmitter/founder-virus lacking the N276 glycan might have initiated the development of these NAbs. Together these data strengthen the rationale for germline-targeting vaccination strategies to induce IOMA-class bNAbs and provide a wealth of sequence and structural information to support such strategies.


    Organizational Affiliation

    Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands. M.J.vangils@amsterdamumc.nl.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AMC009 SOSIPv5.2 envelope glycoprotein gp120A,
C,
E [auth D]
482Human immunodeficiency virus 1Mutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AMC009 SOSIP.v5.2 envelope glycoprotein gp41B,
D [auth E],
F
154Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ACS124 heavy chainG,
K [auth M]
124Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ACS124 light chainH [auth I],
L [auth O]
108Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ACS101 heavy chainI [auth H],
M [auth J],
O [auth K]
126Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ACS101 light chainJ [auth L],
N,
P
108Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
CB [auth 2],
GA [auth g],
JB [auth 9],
KB [auth AA],
LA [auth l],
CB [auth 2],
GA [auth g],
JB [auth 9],
KB [auth AA],
LA [auth l],
Q,
SA [auth s],
UA [auth u],
VA [auth v],
W
2N-Glycosylation Oligosaccharides Interaction
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
DB [auth 3],
EA [auth e],
EB [auth 4],
FA [auth f],
FB [auth 5],
GB [auth 6],
HA [auth h],
HB [auth 7],
IA [auth i],
IB [auth 8],
JA [auth j],
KA [auth k],
MA [auth m],
NA [auth n],
OA [auth o],
PA [auth p],
QA [auth q],
R,
RA [auth r],
T,
TA [auth t],
U,
V,
WA [auth w],
X,
XA [auth x],
Y,
Z,
ZA [auth z]
3N-Glycosylation Oligosaccharides Interaction
Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseS,
YA [auth y]
5N-Glycosylation Oligosaccharides Interaction
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth d]3N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AC [auth D],
BC [auth D],
CC [auth D],
DC [auth D],
EC [auth F],
AC [auth D],
BC [auth D],
CC [auth D],
DC [auth D],
EC [auth F],
FC [auth F],
LB [auth A],
MB [auth A],
NB [auth A],
OB [auth A],
PB [auth A],
QB [auth B],
RB [auth B],
SB [auth B],
TB [auth C],
UB [auth C],
VB [auth C],
WB [auth E],
XB [auth E],
YB [auth D],
ZB [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1115782
Bill & Melinda Gates FoundationUnited StatesINV-002916
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI110657

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references