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- PDB-1qbz: THE CRYSTAL STRUCTURE OF THE SIV GP41 ECTODOMAIN AT 1.47 A -

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Basic information

Entry
Database: PDB / ID: 1qbz
TitleTHE CRYSTAL STRUCTURE OF THE SIV GP41 ECTODOMAIN AT 1.47 A
ComponentsPROTEIN (SIV GP41 ECTODOMAIN)
KeywordsENVELOPE GLYCOPROTEIN / SIV / HIV / GP41 / MEMBRANE FUSION / PEPTIDE INHIBITOR / SIV ENVELOPE GLYCOPROTEIN GP41
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, molecular replacement / Resolution: 1.47 Å
AuthorsYang, Z.-N. / Mueser, T.C. / Kaufman, J. / Stahl, S.J. / Wingfield, P.T. / Hyde, C.C.
CitationJournal: J.Struct.Biol. / Year: 1999
Title: The crystal structure of the SIV gp41 ectodomain at 1.47 A resolution.
Authors: Yang, Z.N. / Mueser, T.C. / Kaufman, J. / Stahl, S.J. / Wingfield, P.T. / Hyde, C.C.
History
DepositionApr 28, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0May 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 16, 2015Group: Atomic model
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SIV GP41 ECTODOMAIN)
B: PROTEIN (SIV GP41 ECTODOMAIN)
C: PROTEIN (SIV GP41 ECTODOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,03810
Polymers43,2943
Non-polymers7447
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11110 Å2
ΔGint-132 kcal/mol
Surface area18020 Å2
MethodPISA
2
A: PROTEIN (SIV GP41 ECTODOMAIN)
B: PROTEIN (SIV GP41 ECTODOMAIN)
C: PROTEIN (SIV GP41 ECTODOMAIN)
hetero molecules

A: PROTEIN (SIV GP41 ECTODOMAIN)
B: PROTEIN (SIV GP41 ECTODOMAIN)
C: PROTEIN (SIV GP41 ECTODOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,07520
Polymers86,5886
Non-polymers1,48814
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area23490 Å2
ΔGint-305 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.124, 47.206, 77.465
Angle α, β, γ (deg.)90.00, 100.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-8002-

HG

21B-8052-

HOH

31C-8090-

HOH

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Components

#1: Protein PROTEIN (SIV GP41 ECTODOMAIN)


Mass: 14431.267 Da / Num. of mol.: 3 / Fragment: SIV GP41 ECTODOMAIN 27-149 / Mutation: C86A, C92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Strain: MAC239 / Cellular location: VIRAL MEMBRANE / Production host: Escherichia coli (E. coli) / References: GenBank: 431600, UniProt: E7CWP5*PLUS
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.8 %
Crystal growpH: 4.25
Details: 14-25% MPD (2-METHYL-2,4- PENTANEDIOL) 140-220 MM NACL, 20-40 MM SODIUM ACETATE, pH 4.25
Crystal grow
*PLUS
pH: 3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
250 mMsodium formate1drop
314-25 %(v/v)MPD1reservoir
4140-220 mM1reservoirNaCl
520-40 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97564
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97564 Å / Relative weight: 1
ReflectionResolution: 1.47→15 Å / Num. obs: 49553 / % possible obs: 89.9 % / Observed criterion σ(I): 0.5 / Redundancy: 8.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.8
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.6 / % possible all: 70.9
Reflection
*PLUS
Num. measured all: 412245
Reflection shell
*PLUS
% possible obs: 78.7 %

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Processing

Software
NameVersionClassification
MLPHAREPHASES DM AMOREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
DMphasing
AMoREphasing
RefinementMethod to determine structure: MIR, molecular replacement
Starting model: POLY ALANINE MODEL (RESIDUES 46-74) OF MMLV TRANSMEMBRANE TRIMERIC CORE (1MOF)

1mof


Resolution: 1.47→15 Å / Num. parameters: 28962 / Num. restraintsaints: 36906 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
Details: NO NCS RESTRAINS WERE APPLIED DURING REFINEMENT CAUTION SHOULD BE TAKEN IN INTERPRETING THOSE RESIDUES WITH EQUIVALENT ISOTROPIC B FACTORS HIGHER THAN 60S.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2462 5 %THIN SHELL
all0.155 49533 --
obs0.152 -5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. V. 91 (1973) 201-228
Refine analyzeNum. disordered residues: 37 / Occupancy sum hydrogen: 2609 / Occupancy sum non hydrogen: 3046
Refinement stepCycle: LAST / Resolution: 1.47→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 21 263 3052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.021
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.076
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(I): 2 / % reflection Rfree: 5 % / Rfactor all: 0.16 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg0.03
LS refinement shell
*PLUS
Rfactor obs: 0.267

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