[English] 日本語
Yorodumi
- PDB-1szt: ATOMIC STRUCTURE OF A THERMOSTABLE SUBDOMAIN OF HIV-1 GP41 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1szt
TitleATOMIC STRUCTURE OF A THERMOSTABLE SUBDOMAIN OF HIV-1 GP41
ComponentsHIV-1 ENVELOPE GLYCOPROTEIN GP41
KeywordsVIRAL PROTEIN / COAT PROTEIN / HIV-1 ENVELOPE GLYCOPROTEIN
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane / plasma membrane
Similarity search - Function
Helix Hairpins - #210 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Env polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.4 Å
AuthorsTan, K. / Lu, M. / Wang, J.-H.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Atomic structure of a thermostable subdomain of HIV-1 gp41.
Authors: Tan, K. / Liu, J. / Wang, J. / Shen, S. / Lu, M.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Core Structure of Gp41 from the HIV Envelope Glycoprotein
Authors: Chan, D.C. / Fass, D. / Berger, J.M. / Kim, P.S.
#2: Journal: Nature / Year: 1997
Title: Atomic Structure of the Ectodomain from HIV-1 Gp41
Authors: Weissenhorn, W. / Dessen, A. / Harrison, S.C. / Skehel, J.J. / Wiley, D.C.
#3: Journal: Nat.Struct.Biol. / Year: 1995
Title: A Trimeric Structural Domain of the HIV-1 Transmembrane Glycoprotein
Authors: Lu, M. / Blacklow, S.C. / Kim, P.S.
History
DepositionJul 28, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 ENVELOPE GLYCOPROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)7,8801
Polymers7,8801
Non-polymers00
Water75742
1
A: HIV-1 ENVELOPE GLYCOPROTEIN GP41

A: HIV-1 ENVELOPE GLYCOPROTEIN GP41

A: HIV-1 ENVELOPE GLYCOPROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)23,6393
Polymers23,6393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6660 Å2
ΔGint-54 kcal/mol
Surface area10860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.070, 53.070, 60.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein HIV-1 ENVELOPE GLYCOPROTEIN GP41 / GP41


Mass: 7879.753 Da / Num. of mol.: 1
Fragment: RESIDUES 546 - 579 AND 628 - 655 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)
Source method: isolated from a genetically manipulated source
Details: CORE OF TRANSMEMBRANE SUBUNIT (GP41) / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus
Description: RECOMBINANT GP41 WITH LINKER (SER-GLY-GLY-ARG-GLY-GLY) BETWEEN TWO FRAGMENTS
Cell line: BL21 / Gene: GP41 / Plasmid: PN41/C34-L6 / Gene (production host): GP41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P04582, UniProt: Q3I1N2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 31 - ...IN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 31 - 40 IS AN ARTIFICIAL LINKER SGGRGG AND 41 - 68 IS GP41 RESIDUES 628 - 655.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 %PEG40001reservoir
30.2 Mammonium sulfate1reservoir
410 %glycerol1reservoir
50.1 M1reservoirNaAc

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 2481 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.61
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 8.98 / % possible all: 99.6
Reflection shell
*PLUS
% possible obs: 99.6 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→15 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.269 -10 %
Rwork0.208 --
obs0.208 2356 -
Displacement parametersBiso mean: 61.06 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms555 0 0 42 597
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.999
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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