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- PDB-1szt: ATOMIC STRUCTURE OF A THERMOSTABLE SUBDOMAIN OF HIV-1 GP41 -

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Basic information

Entry
Database: PDB / ID: 1szt
TitleATOMIC STRUCTURE OF A THERMOSTABLE SUBDOMAIN OF HIV-1 GP41
ComponentsHIV-1 ENVELOPE GLYCOPROTEIN GP41
KeywordsVIRAL PROTEIN / COAT PROTEIN / HIV-1 ENVELOPE GLYCOPROTEIN
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host 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 / 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 / Env polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.4 Å
AuthorsTan, K. / Lu, M. / Wang, J.-H.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Atomic structure of a thermostable subdomain of HIV-1 gp41.
Authors: Tan, K. / Liu, J. / Wang, J. / Shen, S. / Lu, M.
#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.
#2: Journal: Nature / Year: 1997
Title: Atomic Structure of the Ectodomain from HIV-1 Gp41
Authors: Weissenhorn, W. / Dessen, A. / Harrison, S.C. / Skehel, J.J. / Wiley, D.C.
#3: Journal: Nat.Struct.Biol. / Year: 1995
Title: A Trimeric Structural Domain of the HIV-1 Transmembrane Glycoprotein
Authors: Lu, M. / Blacklow, S.C. / Kim, P.S.
History
DepositionJul 28, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 ENVELOPE GLYCOPROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)7,8801
Polymers7,8801
Non-polymers00
Water75742
1
A: HIV-1 ENVELOPE GLYCOPROTEIN GP41

A: HIV-1 ENVELOPE GLYCOPROTEIN GP41

A: HIV-1 ENVELOPE GLYCOPROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)23,6393
Polymers23,6393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6660 Å2
ΔGint-54 kcal/mol
Surface area10860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.070, 53.070, 60.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein HIV-1 ENVELOPE GLYCOPROTEIN GP41 / GP41


Mass: 7879.753 Da / Num. of mol.: 1
Fragment: RESIDUES 546 - 579 AND 628 - 655 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)
Source method: isolated from a genetically manipulated source
Details: CORE OF TRANSMEMBRANE SUBUNIT (GP41) / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus
Description: RECOMBINANT GP41 WITH LINKER (SER-GLY-GLY-ARG-GLY-GLY) BETWEEN TWO FRAGMENTS
Cell line: BL21 / Gene: GP41 / Plasmid: PN41/C34-L6 / Gene (production host): GP41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P04582, UniProt: Q3I1N2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 31 - ...IN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 31 - 40 IS AN ARTIFICIAL LINKER SGGRGG AND 41 - 68 IS GP41 RESIDUES 628 - 655.

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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: 2.08 Å3/Da / Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 %PEG40001reservoir
30.2 Mammonium sulfate1reservoir
410 %glycerol1reservoir
50.1 M1reservoirNaAc

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 2481 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.61
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 8.98 / % possible all: 99.6
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→15 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.269 -10 %
Rwork0.208 --
obs0.208 2356 -
Displacement parametersBiso mean: 61.06 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms555 0 0 42 597
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg0.999
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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