[English] 日本語
Yorodumi
- PDB-9atz: HIV 16055.v8.3 SOSIP Env in Complex with V2 Epitope and Anti-Immu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9atz
TitleHIV 16055.v8.3 SOSIP Env in Complex with V2 Epitope and Anti-Immune Complex pAbs from Rabbit 2464
Components
  • (Rabbit Anti-Immune Complex Antibody - Predicted ...) x 2
  • (Rabbit V2 Polyclonal Antibody - Predicted ...) x 2
  • Surface protein gp120
  • Transmembrane protein gp41
KeywordsVIRAL PROTEIN / HIV / Polyclonal / Antibodies / CryoEMPEM / Rabbit / Anti-Immune Complex / V1/V3
Function / homology
Function and homology information


positive regulation of establishment of T cell polarity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / : / viral envelope ...positive regulation of establishment of T cell polarity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / : / viral envelope / apoptotic process / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBrown, S. / Antansijevic, A. / Ward, A.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Sci Immunol / Year: 2025
Title: Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens.
Authors: Sharidan Brown / Aleksandar Antanasijevic / Leigh M Sewall / Daniel Montiel Garcia / Philip J M Brouwer / Rogier W Sanders / Andrew B Ward /
Abstract: Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody ...Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody responses are directed to easily accessible nonneutralizing epitopes on Env instead of bnAb epitopes. Autologously neutralizing antibody responses appear upon boosting, once immunodominant epitopes are saturated. Here, we use electron microscopy-based polyclonal epitope mapping (EMPEM) to elucidate how repeated immunization with HIV Env SOSIP immunogens results in the generation of Ab2α anti-idiotypic antibodies in rabbits and rhesus macaques. We present the structures of six anti-immune complex antibodies and find that they target idiotopes composed of framework regions of antibodies bound to Env. Examination of cryo-electron microscopy density enabled prediction of sequences for an anti-immune complex antibody, the paratope of which is enriched with aromatic amino acids. This work sheds light on current vaccine development efforts for HIV, as well as for other pathogens in which repeated exposure to antigen is required.
History
DepositionFeb 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rabbit V2 Polyclonal Antibody - Predicted Light Chain
B: Rabbit Anti-Immune Complex Antibody - Predicted Light Chain
C: Rabbit V2 Polyclonal Antibody - Predicted Heavy Chain
D: Surface protein gp120
E: Rabbit Anti-Immune Complex Antibody - Predicted Heavy Chain
F: Rabbit V2 Polyclonal Antibody - Predicted Light Chain
G: Rabbit Anti-Immune Complex Antibody - Predicted Light Chain
H: Rabbit V2 Polyclonal Antibody - Predicted Heavy Chain
I: Surface protein gp120
J: Rabbit Anti-Immune Complex Antibody - Predicted Heavy Chain
K: Rabbit Anti-Immune Complex Antibody - Predicted Light Chain
L: Rabbit V2 Polyclonal Antibody - Predicted Heavy Chain
M: Surface protein gp120
N: Rabbit V2 Polyclonal Antibody - Predicted Light Chain
O: Transmembrane protein gp41
P: Transmembrane protein gp41
Q: Transmembrane protein gp41
R: Rabbit Anti-Immune Complex Antibody - Predicted Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,49064
Polymers343,40118
Non-polymers15,08946
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 2 types, 6 molecules DIMOPQ

#4: Protein Surface protein gp120 / HIV 16055.v8.3 SOSIP gp120


Mass: 58156.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: This sequence contains engineered SOSIP mutations. The construct sequence is not identical to wild type Env. The first thirty residues in the sequence is an expression tag.
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: A1EAI1
#6: Protein Transmembrane protein gp41 / HIV 16055.v8.3 SOSIP gp41


Mass: 17430.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: This sequence contains engineered SOSIP mutations. The construct sequence is not identical to wild type Env.
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: A0A0B5KUY7

-
Antibody , 4 types, 12 molecules AFNBGKCHLEJR

#1: Antibody Rabbit V2 Polyclonal Antibody - Predicted Light Chain


Mass: 9209.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: The sequence of this polyclonal antibody is unknown.
Source: (natural) Oryctolagus cuniculus (rabbit)
#2: Antibody Rabbit Anti-Immune Complex Antibody - Predicted Light Chain


Mass: 9549.763 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: The sequence of this polyclonal antibody is unknown.
Source: (natural) Oryctolagus cuniculus (rabbit)
#3: Antibody Rabbit V2 Polyclonal Antibody - Predicted Heavy Chain


Mass: 10656.127 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: The sequence of this polyclonal antibody is unknown.
Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Antibody Rabbit Anti-Immune Complex Antibody - Predicted Heavy Chain


Mass: 9464.658 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: The sequence of this polyclonal antibody is unknown.
Source: (natural) Oryctolagus cuniculus (rabbit)

-
Sugars , 3 types, 46 molecules

#7: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#9: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestN
Has protein modificationY
Sequence detailsThe antibodies that are part of this complex come from polyclonal sera. As a result, the sequences ...The antibodies that are part of this complex come from polyclonal sera. As a result, the sequences for these antibodies are unknown. They are modeled as a poly-UNK chains.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: HIV-1 16055 SOSIP Env in Complex with Rabbit Polyclonal Antibodies - V2 Epitope and Anti-Immune Complex pAbs
Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
SpecimenConc.: 5.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23375 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421404
ELECTRON MICROSCOPYf_angle_d0.66529307
ELECTRON MICROSCOPYf_dihedral_angle_d9.4226846
ELECTRON MICROSCOPYf_chiral_restr0.0473758
ELECTRON MICROSCOPYf_plane_restr0.0033791

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more