[English] 日本語
Yorodumi
- PDB-6me1: Crystal structure of the clade B isolate B41 mutant fusion peptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6me1
TitleCrystal structure of the clade B isolate B41 mutant fusion peptide (residues 512-521) in complex with VRC34.01
Components
  • Envelope glycoprotein gp160
  • VRC34.01 Fab heavy chain
  • VRC34.01 Fab light chain
KeywordsVIRAL PROTEIN / HIV / ENVELOPE / FUSION PEPTIDE / HIV-1 GP41 / IMMUNE SYSTEM / NEUTRALIZING ANTIBODIES / COMPLEX / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


host cell periphery / CD4 receptor binding / Dectin-2 family / 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 / host cell perinuclear region of cytoplasm / fusion of virus membrane with host plasma membrane ...host cell periphery / CD4 receptor binding / Dectin-2 family / 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 / host cell perinuclear region of cytoplasm / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / 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 speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKumar, S. / Sarkar, A. / Wilson, I.A.
CitationJournal: Nat Commun / Year: 2019
Title: Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide.
Authors: Kumar, S. / Sarkar, A. / Pugach, P. / Sanders, R.W. / Moore, J.P. / Ward, A.B. / Wilson, I.A.
History
DepositionSep 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VRC34.01 Fab heavy chain
B: VRC34.01 Fab light chain
F: Envelope glycoprotein gp160
C: VRC34.01 Fab heavy chain
D: VRC34.01 Fab light chain
E: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)97,3376
Polymers97,3376
Non-polymers00
Water10,305572
1
A: VRC34.01 Fab heavy chain
B: VRC34.01 Fab light chain
F: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)48,6683
Polymers48,6683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-34 kcal/mol
Surface area19750 Å2
MethodPISA
2
C: VRC34.01 Fab heavy chain
D: VRC34.01 Fab light chain
E: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)48,6683
Polymers48,6683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-36 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.421, 123.670, 101.253
Angle α, β, γ (deg.)90.00, 90.87, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody VRC34.01 Fab heavy chain


Mass: 23797.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody VRC34.01 Fab light chain


Mass: 23138.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 1731.958 Da / Num. of mol.: 2 / Fragment: residues 512-521 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03375
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium sulfate, 20%(w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 72903 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.89 / Net I/σ(I): 11.4
Reflection shellResolution: 1.97→2.01 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3639 / CC1/2: 0.64 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I8C

5i8c


Resolution: 1.97→38.18 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.238 3665 5.03 %
Rwork0.1993 --
obs0.2013 72849 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6790 0 0 572 7362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036967
X-RAY DIFFRACTIONf_angle_d0.6169483
X-RAY DIFFRACTIONf_dihedral_angle_d14.5764127
X-RAY DIFFRACTIONf_chiral_restr0.0461071
X-RAY DIFFRACTIONf_plane_restr0.0041210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9679-1.99380.35131350.29952183X-RAY DIFFRACTION81
1.9938-2.02110.28311680.28442712X-RAY DIFFRACTION100
2.0211-2.050.31781600.27192599X-RAY DIFFRACTION100
2.05-2.08060.31361280.26982632X-RAY DIFFRACTION98
2.0806-2.11310.30411480.25582714X-RAY DIFFRACTION99
2.1131-2.14770.26571230.24032656X-RAY DIFFRACTION100
2.1477-2.18470.2631420.23412669X-RAY DIFFRACTION100
2.1847-2.22450.29511270.23592723X-RAY DIFFRACTION100
2.2245-2.26730.29691520.24892521X-RAY DIFFRACTION96
2.2673-2.31350.29911410.22612684X-RAY DIFFRACTION100
2.3135-2.36380.23851550.21792714X-RAY DIFFRACTION100
2.3638-2.41880.27781280.21932677X-RAY DIFFRACTION100
2.4188-2.47930.26791360.21442688X-RAY DIFFRACTION99
2.4793-2.54630.2341300.2092651X-RAY DIFFRACTION99
2.5463-2.62120.2561310.2142718X-RAY DIFFRACTION99
2.6212-2.70580.28281460.22262620X-RAY DIFFRACTION99
2.7058-2.80250.28831420.20952702X-RAY DIFFRACTION99
2.8025-2.91460.23051180.20492687X-RAY DIFFRACTION100
2.9146-3.04720.24431500.20522730X-RAY DIFFRACTION100
3.0472-3.20780.27371250.21122684X-RAY DIFFRACTION100
3.2078-3.40870.2431570.20062680X-RAY DIFFRACTION100
3.4087-3.67170.22821440.18092703X-RAY DIFFRACTION100
3.6717-4.04080.21151280.17912706X-RAY DIFFRACTION99
4.0408-4.62470.19391550.15222689X-RAY DIFFRACTION100
4.6247-5.82320.1951540.16012696X-RAY DIFFRACTION100
5.8232-38.18680.17121420.17792746X-RAY DIFFRACTION99

+
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