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 9BIO | pdb_00009bio

Structure of VRC44.01 Fab in complex with 3BNC117-purified C1080.c3 RnS SOSIP.664 HIV-1 Env trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BIO

This is version 1.2 of the entry. See complete history. 

Literature

A multidonor class of highly glycan-dependent HIV-1 gp120-gp41 interface-targeting broadly neutralizing antibodies.

Cale, E.M., Shen, C.H., Olia, A.S., Radakovich, N.A., Rawi, R., Yang, Y., Ambrozak, D.R., Bennici, A.K., Chuang, G.Y., Crooks, E.D., Driscoll, J.I., Lin, B.C., Louder, M.K., Madden, P.J., Messina, M.A., Osawa, K., Stewart-Jones, G.B.E., Verardi, R., Vrakas, Z., Xie, D., Zhang, B., Binley, J.M., Connors, M., Koup, R.A., Pierson, T.C., Doria-Rose, N.A., Kwong, P.D., Mascola, J.R., Gorman, J.

(2024) Cell Rep 43: 115010-115010

  • DOI: https://doi.org/10.1016/j.celrep.2024.115010
  • Primary Citation Related Structures: 
    9BIO

  • PubMed Abstract: 

    Antibodies that target the gp120-gp41 interface of the HIV-1 envelope (Env) trimer comprise a commonly elicited category of broadly neutralizing antibodies (bNAbs). Here, we isolate and characterize VRC44, a bNAb lineage with up to 52% neutralization breadth. The cryoelectron microscopy (cryo-EM) structure of antibody VRC44.01 in complex with the Env trimer reveals binding to the same gp120-gp41 interface site of vulnerability as antibody 35O22 from a different HIV-1-infected donor. In addition to having similar angles of approach and extensive contacts with glycans N88 and N625, VRC44 and 35O22 derive from the same IGHV1-18 gene and share convergent mutations, indicating these two antibodies to be members of the only known highly glycan-dependent multidonor class. Strikingly, both lineages achieved almost 100% neutralization breadth against virus strains displaying high-mannose glycans. The high breadth and reproducible elicitation of VRC44 and 35O22 lineages validate germline-based methods of immunogen design for targeting the HIV-1 gp120-gp41 interface.


  • Organizational Affiliation: 
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 477.44 kDa 
  • Atom Count: 27,498 
  • Modeled Residue Count: 3,153 
  • Deposited Residue Count: 3,933 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41A [auth B],
G [auth A],
M [auth J]
170Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A0A0R6CVA7 (Human immunodeficiency virus type 1)
Explore A0A0R6CVA7 
Go to UniProtKB:  A0A0R6CVA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R6CVA7
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B [auth G],
H [auth C],
N [auth K]
478Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q1M0K6 (Human immunodeficiency virus type 1)
Explore Q1M0K6 
Go to UniProtKB:  Q1M0K6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1M0K6
Glycosylation
Glycosylation Sites: 20
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
3BNC117 heavy chainC [auth S],
I [auth D],
O [auth M]
226Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
3BNC117 light chainD [auth U],
J [auth E],
P [auth N]
206Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC44.01 light chainE [auth L],
K [auth F],
Q [auth O]
107Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC44.01 heavy chainF [auth H],
L [auth I],
R [auth P]
124Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseGA [auth g],
S [auth Q],
UA [auth u]
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G27389SR
GlyCosmos: G27389SR
GlyGen: G27389SR
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
AB [auth 0],
CA [auth c],
CB [auth 2],
DA [auth d],
AA [auth a],
AB [auth 0],
CA [auth c],
CB [auth 2],
DA [auth d],
EA [auth e],
EB [auth 4],
FA [auth f],
FB [auth 5],
GB [auth 6],
HA [auth h],
IA [auth i],
MA [auth m],
OA [auth o],
QA [auth q],
RA [auth r],
SA [auth s],
T [auth R],
TA [auth t],
U [auth T],
VA [auth v],
WA [auth w],
Y
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseJA [auth j],
V,
XA [auth x]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseKA [auth k],
W,
YA [auth y]
9N-Glycosylation
Glycosylation Resources
GlyTouCan: G68668TB
GlyCosmos: G68668TB
GlyGen: G68668TB
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
DB [auth 3],
LA [auth l],
PA [auth p],
X,
BA [auth b],
DB [auth 3],
LA [auth l],
PA [auth p],
X,
ZA [auth z]
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBB [auth 1],
NA [auth n],
Z
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AC [auth C]
BC [auth C]
CC [auth C]
DC [auth C]
EC [auth E]
AC [auth C],
BC [auth C],
CC [auth C],
DC [auth C],
EC [auth E],
FC [auth J],
GC [auth J],
HB [auth B],
HC [auth K],
IB [auth B],
IC [auth K],
JB [auth B],
JC [auth K],
KB [auth G],
KC [auth K],
LB [auth G],
LC [auth K],
MB [auth G],
MC [auth K],
NB [auth G],
NC [auth K],
OB [auth G],
OC [auth K],
PB [auth G],
PC [auth N],
QB [auth G],
RB [auth G],
SB [auth U],
TB [auth A],
UB [auth A],
WB [auth C],
XB [auth C],
YB [auth C],
ZB [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
VB [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Simons FoundationUnited StatesSF349247

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection
  • Version 1.2: 2025-01-01
    Changes: Data collection, Database references