[English] 日本語
Yorodumi
- PDB-1qce: SOLUTION NMR STRUCTURE OF ECTODOMAIN OF SIV GP41, RESTRAINED REGU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qce
TitleSOLUTION NMR STRUCTURE OF ECTODOMAIN OF SIV GP41, RESTRAINED REGULARIZED MEAN STRUCTURE PLUS 29 SIMULATED ANNEALING STRUCTURES
ComponentsPROTEIN (GP41)
KeywordsVIRAL PROTEIN / VIRUS ENVELOPE PROTEIN / SIV GP41 ECTODOMAIN
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Helix Hairpins - #210 / 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
Similarity search - Component
Biological speciesSimian immunodeficiency virus
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M.
Citation
Journal: J.Am.Chem.Soc. / Year: 1999
Title: Measurement of Residual Dipolar Couplings of Macromolecules Aligned in the Nematic Phase of Acolloidal Suspension of Rod-Shaped Viruses
Authors: Kuszewski, J. / Gronenborn, A.M. / Clore, G.M.
#1: Journal: Embo J. / Year: 1998
Title: Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41.
Authors: Caffrey, M. / Cai, M. / Kaufman, J. / Stahl, S.J. / Wingfield, P.T. / Covell, D.G. / Gronenborn, A.M. / Clore, G.M.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: Determination of the secondary structure and global topology of the 44 kDa ectodomain of gp41 of the simian immunodeficiency virus by multidimensional nuclear magnetic resonance spectroscopy.
Authors: Caffrey, M. / Cai, M. / Kaufman, J. / Stahl, S.J. / Wingfield, P.T. / Gronenborn, A.M. / Clore, G.M.
History
DepositionApr 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (GP41)
B: PROTEIN (GP41)
C: PROTEIN (GP41)


Theoretical massNumber of molelcules
Total (without water)43,2943
Polymers43,2943
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11690 Å2
ΔGint-84 kcal/mol
Surface area20340 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30
RepresentativeModel #1restraine minimized mean coordinates

-
Components

#1: Protein PROTEIN (GP41)


Mass: 14431.267 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN, RESIDUES 27 - 149, NUMBERED 1 - 123 / Source method: isolated from a natural source / Source: (natural) Simian immunodeficiency virus / Genus: Lentivirus / Strain: SOOTEY MANGABEY / References: UniProt: Q88031
Sequence details1QCE A GB 431487 1 - 551 NOT IN ATOMS LIST 1QCE A GB 431487 675 - 876 NOT IN ATOMS LIST 1QCE B GB ...1QCE A GB 431487 1 - 551 NOT IN ATOMS LIST 1QCE A GB 431487 675 - 876 NOT IN ATOMS LIST 1QCE B GB 431487 1 - 551 NOT IN ATOMS LIST 1QCE B GB 431487 675 - 876 NOT IN ATOMS LIST 1QCE C GB 431487 1 - 551 NOT IN ATOMS LIST 1QCE C GB 431487 675 - 876 NOT IN ATOMS LIST

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: D-HNCA
121D-HNCO
131D-HN(CO) CA
141D-HN(CA)CO D-HN(CA)CB
151D-HN(COCA)CB
161D-HN(CA) CB
171D-C(CC)(CO)NH
181HBHA(CO)NH
191HCACO
1101HNCO
1111HNHA
1121(H)CCH-COSY
1131(H)CCH- TOCSY
11414D (H)CCH 13C-13C NOE
1151QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
11613D 15N- SEPARATED NOE AND ROE
11713D 13C-SEPARATED NOE
11813D 13C-SEPARATED/12C FILTERED NOE
11913D 13C- SEPARATED/15N-FILTERED NOE
12013D 15N-SEPARATED/ 13C-FILTERED NOE
12114D 15N/15N-SEPARATED NOE
12214D 15N/13C-SEPARATED NOE AND 4D 13C/13C-SEPARATED NOE EXPERIMENTS
12313D HCA(CO)N FOR THREE-BOND AMIDE DEUTERIUM ISOTOPE SHIFTS

-
Sample preparation

Sample conditionspH: 3 / Temperature: 322.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DMX750BrukerDMX7507503

-
Processing

NMR software
NameClassification
CNS/XPLORrefinement
XPLOR/CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: TERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING: NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS 3JHNALPHA COUPLING CONSTANT RESTRAINTS AND THREE_BOND DEUTERIUMCALPHA(ND) ISOTOPE ...Details: TERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING: NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS 3JHNALPHA COUPLING CONSTANT RESTRAINTS AND THREE_BOND DEUTERIUMCALPHA(ND) ISOTOPE RESTRAINTS (GARRETT ET AL J. MAGN. RESON. B104, 99-103 (1994)). 13CALPHA AND 13CBETA CHEMISCAL SHIFT RESTRAINTS (KUSZEWSKI ET AL J> MAGN RESON B106, 92-96 (1995)) TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI J, GRONENB CLORE, GM J AM CHEM SOC 121, 2337-2338 (1999)) TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI J, GRONEN CLORE GM. PROTEIN SCI 5, 1067-1080 (1996); J. MAGN 125, 171-177 (1997)). COVALENT GEOMETRY RESTRAINTS (BONDS, ANGLES, IMPROPER QUARTIC VAN DER WAALS REPULSION TERM (NILGES. M, GRONENBORN, A.M., BRUNGER, A.T., CLORE, G.M. (1988) PROTEIN ENG. 2, 27-38).
NMR representativeSelection criteria: restraine minimized mean coordinates
NMR ensembleConformers calculated total number: 30 / Conformers submitted total number: 30

+
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