[English] 日本語
Yorodumi
- PDB-6wwc: Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wwc
TitleVaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with S48K mutation in light chain in complex with HIV fusion peptide (residue 512-519)
Components
  • fusion peptide
  • vFP16.02 antibody heavy chain
  • vFP16.02 antibody light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV / fusion peptide / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.563 Å
AuthorsXu, K. / Wang, Y. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody.
Authors: Madan, B. / Zhang, B. / Xu, K. / Chao, C.W. / O'Dell, S. / Wolfe, J.R. / Chuang, G.Y. / Fahad, A.S. / Geng, H. / Kong, R. / Louder, M.K. / Nguyen, T.D. / Rawi, R. / Schon, A. / Sheng, Z. / ...Authors: Madan, B. / Zhang, B. / Xu, K. / Chao, C.W. / O'Dell, S. / Wolfe, J.R. / Chuang, G.Y. / Fahad, A.S. / Geng, H. / Kong, R. / Louder, M.K. / Nguyen, T.D. / Rawi, R. / Schon, A. / Sheng, Z. / Nimrania, R. / Wang, Y. / Zhou, T. / Lin, B.C. / Doria-Rose, N.A. / Shapiro, L. / Kwong, P.D. / DeKosky, B.J.
History
DepositionMay 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: vFP16.02 antibody heavy chain
B: vFP16.02 antibody light chain
C: fusion peptide
D: vFP16.02 antibody heavy chain
F: fusion peptide
H: vFP16.02 antibody light chain


Theoretical massNumber of molelcules
Total (without water)95,9736
Polymers95,9736
Non-polymers00
Water1,946108
1
A: vFP16.02 antibody heavy chain
B: vFP16.02 antibody light chain
C: fusion peptide


Theoretical massNumber of molelcules
Total (without water)47,9873
Polymers47,9873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-38 kcal/mol
Surface area19480 Å2
MethodPISA
2
D: vFP16.02 antibody heavy chain
F: fusion peptide
H: vFP16.02 antibody light chain


Theoretical massNumber of molelcules
Total (without water)47,9873
Polymers47,9873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-37 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.628, 70.526, 93.292
Angle α, β, γ (deg.)90.000, 94.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain H
13chain C
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPROPROchain AAA1 - 2171 - 217
21GLNGLNPROPROchain DDD1 - 2171 - 217
12ASPASPGLUGLUchain BBB1 - 2181 - 218
22ASPASPGLUGLUchain HHF1 - 2181 - 218
13ALAALAPHEPHEchain CCC512 - 5191 - 8
23ALAALAPHEPHEchain FFE512 - 5191 - 8

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody vFP16.02 antibody heavy chain


Mass: 23073.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody vFP16.02 antibody light chain


Mass: 24179.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide fusion peptide


Mass: 732.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl, pH 8.5, 30% v/v PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23890 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.083 / Rrim(I) all: 0.15 / Χ2: 0.749 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.642.90.43811520.8570.2890.5270.47194.2
2.64-2.6930.37611890.8960.2450.450.49898.2
2.69-2.7430.37411910.8870.2450.4480.48598.8
2.74-2.83.10.30712260.910.2010.3680.51699.2
2.8-2.863.10.29711870.9320.1950.3570.55498.8
2.86-2.933.20.26512040.940.1720.3170.5499.1
2.93-33.10.23511980.9510.1540.2820.55999
3-3.083.10.20512070.9660.1360.2470.58198.6
3.08-3.1730.18712020.9520.1250.2260.61998.6
3.17-3.282.90.16412190.9630.1130.2010.6698.6
3.28-3.392.90.15111960.9730.1030.1840.65598.8
3.39-3.5330.13511770.9670.0910.1630.8197
3.53-3.693.10.11711850.9770.0760.140.81897.4
3.69-3.883.20.10111980.9820.0660.1220.89497.2
3.88-4.133.30.09312000.9870.060.1120.97598.5
4.13-4.453.20.08311810.9870.0550.11.01896.6
4.45-4.8930.0811780.9770.0570.0991.07594.5
4.89-5.630.07311830.9870.0510.090.97895.3
5.6-7.052.70.06811900.9910.0490.0840.93895.9
7.05-503.10.04512270.9960.0290.0541.26995.2

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CDO

6cdo


Resolution: 2.563→35.263 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1108 4.64 %
Rwork0.2092 22766 -
obs0.2117 23874 83.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.71 Å2 / Biso mean: 42.9783 Å2 / Biso min: 22.1 Å2
Refinement stepCycle: final / Resolution: 2.563→35.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 0 108 6814
Biso mean---38.8 -
Num. residues----878
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1278X-RAY DIFFRACTION4.804TORSIONAL
12D1278X-RAY DIFFRACTION4.804TORSIONAL
21B1314X-RAY DIFFRACTION4.804TORSIONAL
22H1314X-RAY DIFFRACTION4.804TORSIONAL
31C42X-RAY DIFFRACTION4.804TORSIONAL
32F42X-RAY DIFFRACTION4.804TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5634-2.68010.4294440.308887126
2.6801-2.82130.32291030.2814211762
2.8213-2.9980.28851600.2616303089
2.998-3.22930.3181710.2429334199
3.2293-3.5540.29091560.2215335698
3.554-4.06770.25021630.2001335398
4.0677-5.12230.23331550.1706330896
5.1223-35.260.2361560.1919339096

+
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