[English] 日本語
Yorodumi
- PDB-6vu2: M1214_N1 Fab structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vu2
TitleM1214_N1 Fab structure
Components
  • M1214 N1 Fab heavy chain
  • M1214 N1 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / gp120
Biological speciesHuman immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsPan, R. / Kong, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145655 United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: VSV-Displayed HIV-1 Envelope Identifies Broadly Neutralizing Antibodies Class-Switched to IgG and IgA.
Authors: Manxue Jia / Rachel A Liberatore / Yicheng Guo / Kun-Wei Chan / Ruimin Pan / Hong Lu / Eric Waltari / Eva Mittler / Kartik Chandran / Andrés Finzi / Daniel E Kaufmann / Michael S Seaman / ...Authors: Manxue Jia / Rachel A Liberatore / Yicheng Guo / Kun-Wei Chan / Ruimin Pan / Hong Lu / Eric Waltari / Eva Mittler / Kartik Chandran / Andrés Finzi / Daniel E Kaufmann / Michael S Seaman / David D Ho / Lawrence Shapiro / Zizhang Sheng / Xiang-Peng Kong / Paul D Bieniasz / Xueling Wu /
Abstract: The HIV-1 envelope (Env) undergoes conformational changes during infection. Broadly neutralizing antibodies (bNAbs) are typically isolated by using soluble Env trimers, which do not capture all Env ...The HIV-1 envelope (Env) undergoes conformational changes during infection. Broadly neutralizing antibodies (bNAbs) are typically isolated by using soluble Env trimers, which do not capture all Env states. To address these limitations, we devised a vesicular stomatitis virus (VSV)-based probe to display membrane-embedded Env trimers and isolated five bNAbs from two chronically infected donors, M4008 and M1214. Donor B cell receptor (BCR) repertoires identified two bNAb lineages, M4008_N1 and M1214_N1, that class-switched to immunoglobulin G (IgG) and IgA. Variants of these bNAbs reconstituted as IgA demonstrated broadly neutralizing activity, and the IgA fraction of M1214 plasma conferred neutralization. M4008_N1 epitope mapping revealed a glycan-independent V3 epitope conferring tier 2 virus neutralization. A 4.86-Å-resolution cryogenic electron microscopy (cryo-EM) structure of M1214_N1 complexed with CH505 SOSIP revealed another elongated epitope, the V2V5 corridor, extending from V2 to V5. Overall, the VSV probe identified bNAb lineages with neutralizing IgG and IgA members targeting distinct sites of HIV-1 Env vulnerability.
History
DepositionFeb 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 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 1.3Oct 23, 2024Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: M1214 N1 Fab heavy chain
L: M1214 N1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)46,5542
Polymers46,5542
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-23 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.692, 66.888, 70.176
Angle α, β, γ (deg.)90.000, 108.705, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Antibody M1214 N1 Fab heavy chain


Mass: 23805.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Production host: Homo sapiens (human)
#2: Antibody M1214 N1 Fab light chain


Mass: 22748.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 28% PEG8000, 1.6M calcium acetate and 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920103 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920103 Å / Relative weight: 1
ReflectionResolution: 2.19→29.35 Å / Num. obs: 21766 / % possible obs: 95.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.045 / Rrim(I) all: 0.075 / Net I/σ(I): 10.6
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 1621 / CC1/2: 0.771 / CC star: 0.933 / Rpim(I) all: 0.326 / Rrim(I) all: 0.525 / % possible all: 72

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDS1.16_3549data reduction
XDS1.16_3549data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TSC

4tsc


Resolution: 2.19→29.35 Å / SU ML: 0.2989 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.7985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 1907 5.04 %
Rwork0.1767 35894 -
obs0.1787 21759 84.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.38 Å2
Refinement stepCycle: LAST / Resolution: 2.19→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 0 187 3445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683340
X-RAY DIFFRACTIONf_angle_d0.86774549
X-RAY DIFFRACTIONf_chiral_restr0.0518505
X-RAY DIFFRACTIONf_plane_restr0.0054585
X-RAY DIFFRACTIONf_dihedral_angle_d15.80481987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.3565860.32461567X-RAY DIFFRACTION51.9
2.25-2.310.3783970.28831968X-RAY DIFFRACTION64.81
2.31-2.380.31041360.26192408X-RAY DIFFRACTION80.71
2.38-2.450.30451340.23712618X-RAY DIFFRACTION86.16
2.45-2.540.28541470.21562772X-RAY DIFFRACTION90.23
2.54-2.640.23161470.2112716X-RAY DIFFRACTION90.06
2.64-2.760.26551470.21452725X-RAY DIFFRACTION90.37
2.76-2.910.28691320.20072771X-RAY DIFFRACTION90.27
2.91-3.090.24871530.18252684X-RAY DIFFRACTION89.52
3.09-3.330.20011360.17642635X-RAY DIFFRACTION86.27
3.33-3.660.19631390.1552709X-RAY DIFFRACTION89.64
3.66-4.190.19481480.14092808X-RAY DIFFRACTION92.17
4.19-5.280.14111550.13432745X-RAY DIFFRACTION91.66
5.28-29.350.19651500.1732768X-RAY DIFFRACTION91.07

+
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