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- PDB-2ezr: SOLUTION NMR STRUCTURE OF ECTODOMAIN OF SIV GP41, MODELS 21-30 OF... -

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Basic information

Entry
Database: PDB / ID: 2ezr
TitleSOLUTION NMR STRUCTURE OF ECTODOMAIN OF SIV GP41, MODELS 21-30 OF AN ENSEMBLE OF 40 SIMULATED ANNEALING STRUCTURES
ComponentsGP41
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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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
AuthorsCaffrey, M. / Gronenborn, A.M. / Clore, G.M.
Citation
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.
#1: 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
DepositionMay 20, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP41
B: GP41
C: 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_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40
Representative

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Components

#1: 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: Q88033

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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
12314D 13C/13C-SEPARATED NOE EXPERIMENTS: 3D HCA(CO)N FOR THREE-BOND AMIDE DEUTERIUM ISOTOPE SHIFTS;

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Sample preparation

Sample conditionspH: 3 / Temperature: 322 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

Software
NameClassification
CNSrefinement
CNSphasing
NMR software
NameClassification
CNSstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: NO REFINEMENT WAS DONE
NMR ensembleConformers calculated total number: 40 / Conformers submitted total number: 10

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