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- PDB-1f23: CONTRIBUTION OF A BURIED HYDROGEN BOND TO HIV-1 ENVELOPE GLYCOPRO... -

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Basic information

Entry
Database: PDB / ID: 1f23
TitleCONTRIBUTION OF A BURIED HYDROGEN BOND TO HIV-1 ENVELOPE GLYCOPROTEIN STRUCTURE AND FUNCTION
ComponentsTRANSMEMBRANE GLYCOPROTEIN
KeywordsVIRAL PROTEIN / HIV-1 envelope protein / gp41 / membrane fusion / HIV-1 entry
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / 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 / plasma 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
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsLiu, J. / Shu, W. / Fagan, M. / Nunberg, J.H. / Lu, M.
CitationJournal: Biochemistry / Year: 2001
Title: Structural and functional analysis of the HIV gp41 core containing an Ile573 to Thr substitution: implications for membrane fusion.
Authors: Liu, J. / Shu, W. / Fagan, M.B. / Nunberg, J.H. / Lu, M.
History
DepositionMay 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSMEMBRANE GLYCOPROTEIN
B: TRANSMEMBRANE GLYCOPROTEIN
C: TRANSMEMBRANE GLYCOPROTEIN
D: TRANSMEMBRANE GLYCOPROTEIN
E: TRANSMEMBRANE GLYCOPROTEIN
F: TRANSMEMBRANE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)52,9256
Polymers52,9256
Non-polymers00
Water4,882271
1
A: TRANSMEMBRANE GLYCOPROTEIN
B: TRANSMEMBRANE GLYCOPROTEIN
C: TRANSMEMBRANE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)26,4623
Polymers26,4623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-61 kcal/mol
Surface area10600 Å2
MethodPISA
2
D: TRANSMEMBRANE GLYCOPROTEIN
E: TRANSMEMBRANE GLYCOPROTEIN
F: TRANSMEMBRANE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)26,4623
Polymers26,4623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-60 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.920, 41.870, 55.980
Angle α, β, γ (deg.)90.59, 88.93, 96.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
TRANSMEMBRANE GLYCOPROTEIN / GP41


Mass: 8820.789 Da / Num. of mol.: 6 / Fragment: ECTODOMAIN / Mutation: I28T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: PN36(L)C34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89797
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium citrate, PEG 4000, propanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Msodium citrate1reservoir
35 %propanol1reservoir
47 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 24, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 14667 / Num. obs: 14667 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.287 / Num. unique all: 1399 / % possible all: 92.8
Reflection
*PLUS
Num. measured all: 62249

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 730014.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1493 10.2 %RANDOM
Rwork0.191 ---
all-14667 --
obs-14667 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.82 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å21.72 Å21.71 Å2
2--4.67 Å22.26 Å2
3----5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 0 271 3761
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d15.9
X-RAY DIFFRACTIONc_improper_angle_d0.61
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 229 10.8 %
Rwork0.239 1899 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.191 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.61
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.35 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.239

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