[English] 日本語
Yorodumi
- PDB-6vor: Crystal structure of macaque anti-HIV-1 antibody RM20E1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vor
TitleCrystal structure of macaque anti-HIV-1 antibody RM20E1
Components
  • RM20E1 Fab heavy chain
  • RM20E1 Fab light chain
KeywordsIMMUNE SYSTEM / HIV / antibody / non-human primates
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / GLYCINE
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: PLoS Pathog / Year: 2020
Title: Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates.
Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / ...Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / Raj Patel / Justin Gross / Leigh M Sewall / Jeffrey Copps / Gabriel Ozorowski / Bartek Nogal / Devin Sok / Eva G Rakasz / Celia Labranche / Vladimir Vigdorovich / Scott Christley / Diane G Carnathan / D Noah Sather / David Montefiori / Guido Silvestri / Dennis R Burton / John P Moore / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils /
Abstract: The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown ...The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.
History
DepositionJan 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RM20E1 Fab heavy chain
B: RM20E1 Fab light chain
C: RM20E1 Fab heavy chain
D: RM20E1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5916
Polymers97,4414
Non-polymers1502
Water5,765320
1
A: RM20E1 Fab heavy chain
B: RM20E1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers48,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-21 kcal/mol
Surface area20580 Å2
MethodPISA
2
C: RM20E1 Fab heavy chain
D: RM20E1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8714
Polymers48,7202
Non-polymers1502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.369, 57.741, 92.745
Angle α, β, γ (deg.)98.740, 94.050, 97.830
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody RM20E1 Fab heavy chain


Mass: 24589.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody RM20E1 Fab light chain


Mass: 24130.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: The RM20E1 Fab was crystallized from a solution containing 6.3 mg/mL protein in 1X TBS with a well solution containing 0.1M glycine, pH 10.5, 1.2M NaH2PO4, 0.8M Na2HPO4, and 0.2M Li2SO4, ...Details: The RM20E1 Fab was crystallized from a solution containing 6.3 mg/mL protein in 1X TBS with a well solution containing 0.1M glycine, pH 10.5, 1.2M NaH2PO4, 0.8M Na2HPO4, and 0.2M Li2SO4, with 15% ethylene glycol supplemented as cryoprotectant.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 142088 / % possible obs: 85.4 % / Redundancy: 2.7 % / CC1/2: 0.916 / Net I/σ(I): 18.8
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 2413 / CC1/2: 0.56

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IT2

5it2


Resolution: 1.85→32.628 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 36.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1982 2.61 %
Rwork0.224 73983 -
obs0.2247 75965 76.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.35 Å2 / Biso mean: 39.2758 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 1.85→32.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6710 0 10 320 7040
Biso mean--40.93 39.96 -
Num. residues----871
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.89630.4168540.4397217632
1.8963-1.94750.3715740.3528271740
1.9475-2.00480.3507790.3402323247
2.0048-2.06950.3694990.3202383455
2.0695-2.14350.31951250.3098427162
2.1435-2.22930.28941250.3005491371
2.2293-2.33070.35851520.3133575884
2.3307-2.45360.32471740.2769647594
2.4536-2.60720.28041830.2816679698
2.6072-2.80840.30411780.2688667997
2.8084-3.09090.30721890.2524683099
3.0909-3.53770.25891830.2196682099
3.5377-4.45530.20641870.1743669897
4.4553-32.6280.18481800.1649678499

+
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