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- PDB-2siv: SIV GP41 CORE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 2siv
TitleSIV GP41 CORE STRUCTURE
Components(SIV GP41 GLYCOPROTEIN) x 2
KeywordsENVELOPE GLYCOPROTEIN / RETROVIRUS / HIV / SIV / GP41 / COAT PROTEIN
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 / membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Env polyprotein / Env polyprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesSimian immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMalashkevich, V.N. / Chan, D.C. / Chutkowski, C.T. / Kim, P.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of the simian immunodeficiency virus (SIV) gp41 core: conserved helical interactions underlie the broad inhibitory activity of gp41 peptides.
Authors: Malashkevich, V.N. / Chan, D.C. / Chutkowski, C.T. / Kim, P.S.
#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.
History
DepositionJun 17, 1998Processing site: BNL
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIV GP41 GLYCOPROTEIN
B: SIV GP41 GLYCOPROTEIN
C: SIV GP41 GLYCOPROTEIN
D: SIV GP41 GLYCOPROTEIN
E: SIV GP41 GLYCOPROTEIN
F: SIV GP41 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)25,5866
Polymers25,5866
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-83 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.722, 57.713, 66.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.997495, 0.030635, 0.063762), (0.068623, -0.637871, -0.76708), (0.017172, 0.769534, -0.638375)-0.61806, 4.72568, 9.06871
2given(0.997852, 0.06516, -0.006749), (0.034627, -0.437199, 0.898698), (0.055608, -0.897001, -0.438516)0.3764, -4.14261, 8.52557
3given(0.993118, -0.059416, 0.100926), (0.031675, -0.693376, -0.71988), (0.112752, 0.718122, -0.686722)-1.3587, 4.19844, 5.67586
4given(0.984594, -0.138165, 0.107169), (-0.100742, 0.052722, 0.993515), (-0.142919, -0.989005, 0.03799)-2.1036, 3.73381, 8.69652

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Components

#1: Protein/peptide SIV GP41 GLYCOPROTEIN / N36/C34 CORE


Mass: 4218.902 Da / Num. of mol.: 3 / Fragment: PROTEASE-RESISTANT CORE
Source method: isolated from a genetically manipulated source
Details: N36 AND C34 ARE SYNTHETIC PEPTIDES / Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Gene: GP41 / References: UniProt: Q87973, UniProt: Q8AKX0*PLUS
#2: Protein/peptide SIV GP41 GLYCOPROTEIN / N36/C34 CORE


Mass: 4309.762 Da / Num. of mol.: 3 / Fragment: PROTEASE-RESISTANT CORE
Source method: isolated from a genetically manipulated source
Details: N36 AND C34 ARE SYNTHETIC PEPTIDES / Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Strain: MAC239 / Cellular location: VIRAL MEMBRANE / Gene: GP41 / References: UniProt: Q87973, UniProt: Q52SW3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 %
Description: CRYSTAL DEMONSTRATED HIGH MOSAICITY (1.2 DEGREES) AND ANISOTROPIC DIFFRACTION
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 18-19% PEG8000, 0.1 M SODIUM CACODILATE PH 6.5, 0.2 M MG-ACETATE
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
218-19 %PEG80001reservoir
30.1 Msodium cacodylate1reservoir
40.2 Mmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: YALE MIRRORS
RadiationMonochromator: NICKEL FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 11157 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 23.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.244 / % possible all: 88.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 52353

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AIK

1aik


Resolution: 2.2→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1068 9.8 %RANDOM
Rwork0.211 ---
obs0.211 10857 95.7 %-
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1--9.45 Å20 Å20 Å2
2---3.42 Å20 Å2
3---12.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 0 184 1993
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.53.3
X-RAY DIFFRACTIONx_mcangle_it24.2
X-RAY DIFFRACTIONx_scbond_it24.7
X-RAY DIFFRACTIONx_scangle_it2.56.2
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 144 8.7 %
Rwork0.33 1519 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65
LS refinement shell
*PLUS
Rfactor Rwork: 0.33

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