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- PDB-2x7r: Crystal structure of a late fusion intermediate of HIV-1 gp41 -

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Basic information

Entry
Database: PDB / ID: 2x7r
TitleCrystal structure of a late fusion intermediate of HIV-1 gp41
Components(TRANSMEMBRANE PROTEIN GP41) x 2
KeywordsVIRAL PROTEIN / ENVELOPE GLYCOPROTEIN / MEMBRANE ANCHORED FUSION PROTEIN
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Helix Hairpins - #210 / Envelope glycoprotein Gp160 / 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1 LW12.3 ISOLATE
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNatrajan, G. / Buzon, V. / Weissenhorn, W.
CitationJournal: Plos Pathog. / Year: 2010
Title: Crystal Structure of HIV-1 Gp41 Including Both Fusion Peptide and Membrane Proximal External Regions.
Authors: Buzon, V. / Natrajan, G. / Schibli, D. / Campelo, F. / Kozlov, M.M. / Weissenhorn, W.
History
DepositionMar 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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: TRANSMEMBRANE PROTEIN GP41
B: TRANSMEMBRANE PROTEIN GP41
C: TRANSMEMBRANE PROTEIN GP41
D: TRANSMEMBRANE PROTEIN GP41
E: TRANSMEMBRANE PROTEIN GP41
N: TRANSMEMBRANE PROTEIN GP41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,09510
Polymers43,9906
Non-polymers1044
Water1,00956
1
C: TRANSMEMBRANE PROTEIN GP41
N: TRANSMEMBRANE PROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)14,6632
Polymers14,6632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-17 kcal/mol
Surface area9160 Å2
MethodPISA
2
D: TRANSMEMBRANE PROTEIN GP41
E: TRANSMEMBRANE PROTEIN GP41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7224
Polymers14,6632
Non-polymers582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-30.5 kcal/mol
Surface area8340 Å2
MethodPISA
3
A: TRANSMEMBRANE PROTEIN GP41
B: TRANSMEMBRANE PROTEIN GP41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7094
Polymers14,6632
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-16.9 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.422, 57.422, 182.768
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

21A-2004-

HOH

31D-2009-

HOH

41D-2012-

HOH

51N-2003-

HOH

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Components

#1: Protein TRANSMEMBRANE PROTEIN GP41


Mass: 6837.859 Da / Num. of mol.: 3 / Fragment: EXTRA CELLULAR DOMAIN, RESIDUES 534-581
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 LW12.3 ISOLATE
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA3 (DE3) / References: UniProt: P04578, UniProt: Q70626*PLUS
#2: Protein TRANSMEMBRANE PROTEIN GP41


Mass: 7825.539 Da / Num. of mol.: 3 / Fragment: EXTRA CELLULAR DOMAIN, RESIDUES 629-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 LW12.3 ISOLATE
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA3 (DE3) / References: UniProt: P04578, UniProt: Q70626*PLUS
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.05 Å3/Da / Density % sol: 40.16 % / Description: NONE
Crystal growpH: 6 / Details: 0.1M CITRIC ACID PH 6, 60% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 1, 2009 / Details: TOROIDAL
RadiationMonochromator: CHANNEL CUT ESRF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.505
ReflectionResolution: 2→91.38 Å / Num. obs: 22184 / % possible obs: 96.5 % / Observed criterion σ(I): 2.2 / Redundancy: 5.9 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.8 / % possible all: 84

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AIK

1aik


Resolution: 2→49.729 Å / σ(F): 1.48 / Phase error: 21.27 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2138 1149 5.2 %
Rwork0.1769 --
obs0.1788 22145 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 87.855 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3811 Å20 Å2-0 Å2
2--1.3811 Å20 Å2
3----3.4771 Å2
Refinement stepCycle: LAST / Resolution: 2→49.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 4 56 2510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082514
X-RAY DIFFRACTIONf_angle_d1.1193403
X-RAY DIFFRACTIONf_dihedral_angle_d20.539939
X-RAY DIFFRACTIONf_chiral_restr0.075377
X-RAY DIFFRACTIONf_plane_restr0.003440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.0910.2421390.21322201X-RAY DIFFRACTION78
2.091-2.20090.2241310.19162536X-RAY DIFFRACTION87
2.2009-2.33840.22711440.192597X-RAY DIFFRACTION92
2.3384-2.51830.22341470.18142713X-RAY DIFFRACTION95
2.5183-2.77040.21481440.18012727X-RAY DIFFRACTION95
2.7704-3.16850.22591320.17962744X-RAY DIFFRACTION95
3.1685-3.98120.19231510.14632707X-RAY DIFFRACTION95
3.9812-15.72880.21051520.18162734X-RAY DIFFRACTION94

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