9B8C | pdb_00009b8c

RM018 Fab in complex with Apex GT 6.2 trimer and RM20A3 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9B8C

This is version 1.1 of the entry. See complete history

Literature

HIV broadly neutralizing antibody precursors to the Apex epitope induced in nonhuman primates.

Ma, K.M.Sutton, H.J.Pratap, P.P.Steichen, J.M.Carnathan, D.Quinn, J.Kalyuzhniy, O.Liguori, A.Agrawal, S.Baboo, S.Madden, P.Cottrell, C.A.Willis, J.R.Lee, J.H.Landais, E.Hu, X.Ramezani-Rad, P.Ozorowski, G.Lewis, V.R.Diedrich, J.K.Zhou, X.Altheide, T.K.Phelps, N.Georgeson, E.Alavi, N.B.Lu, D.Eskandarzadeh, S.Kubitz, M.Adachi, Y.Mullen, T.M.Silva, M.Melo, M.B.Himansu, S.Irvine, D.J.Burton, D.R.Yates 3rd, J.R.Paulson, J.C.Sok, D.Wilson, I.A.Silvestri, G.Ward, A.B.Crotty, S.Schief, W.R.

(2025) Sci Immunol 10: eadt6660-eadt6660

  • DOI: https://doi.org/10.1126/sciimmunol.adt6660
  • Primary Citation Related Structures: 
    9B8B, 9B8C, 9MPB, 9MPC, 9MPX, 9MQG

  • PubMed Abstract: 

    An effective prophylactic HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). bnAbs to the Apex region of the HIV envelope glycoprotein (Env) are promising targets for vaccination because of their relatively low somatic hypermutation compared with other bnAbs. Most Apex bnAbs engage Env using an exceptionally long heavy-chain complementarity-determining region 3 (HCDR3) containing specific binding motifs, which reduces bnAb precursor frequency and makes priming of rare bnAb precursors a likely limiting step in the path to Apex bnAb induction. We found that adjuvanted protein or mRNA lipid nanoparticle (LNP) immunization of rhesus macaques with ApexGT6, an Env trimer engineered to bind Apex bnAb precursors, consistently induced Apex bnAb-related precursors with long HCDR3s bearing bnAb-like sequence motifs. Cryo-electron microscopy revealed that elicited Apex bnAb-related HCDR3s had structures combining elements of several prototype Apex bnAbs. These results achieve a critical HIV vaccine development milestone in outbred primates.


  • Organizational Affiliation
    • Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 343 kDa 
  • Atom Count: 20,899 
  • Modeled Residue Count: 2,556 
  • Deposited Residue Count: 2,969 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120
A, C, D
467Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 17
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane protein gp41
B, E, F
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
RM20A3 fragment antigen binding light chain
G, J, N
128Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
RM018 fragment antigen binding heavy chain134Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
RM20A3 fragment antigen binding heavy chain
I, K, M
125Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
RM018 fragment antigen binding light chain216Macaca mulattaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
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-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
O
8N-Glycosylation
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
P, Q, R, S, U
P, Q, R, S, U, V, W
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 9
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-glucopyranose
T, X
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth C]
BA [auth A]
BB [auth D]
CA [auth A]
AA [auth A],
AB [auth C],
BA [auth A],
BB [auth D],
CA [auth A],
CB [auth D],
DA [auth A],
DB [auth D],
EA [auth A],
EB [auth D],
FA [auth A],
FB [auth D],
GA [auth A],
GB [auth D],
HA [auth A],
HB [auth D],
IA [auth A],
IB [auth D],
JA [auth A],
JB [auth D],
KA [auth A],
KB [auth D],
LA [auth A],
LB [auth D],
MA [auth B],
MB [auth D],
NA [auth B],
NB [auth D],
OA [auth B],
OB [auth E],
PA [auth C],
PB [auth E],
QA [auth C],
QB [auth E],
RA [auth C],
RB [auth F],
SA [auth C],
SB [auth F],
TA [auth C],
TB [auth F],
UA [auth C],
VA [auth C],
WA [auth C],
XA [auth C],
Y [auth A],
YA [auth C],
Z [auth A],
ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
H
L-PEPTIDE LINKINGC9 H11 N O6 STYR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-002916
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI144462

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references