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- PDB-1qce: SOLUTION NMR STRUCTURE OF ECTODOMAIN OF SIV GP41, RESTRAINED REGU... -

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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 / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
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

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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

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Experimental details

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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

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Sample preparation

Sample conditionspH: 3.00 / Temperature: 322.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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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

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