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- PDB-3g9r: Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region i... -

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Entry
Database: PDB / ID: 3g9r
TitleStructure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation
ComponentsFusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
KeywordsVIRAL PROTEIN / gp41 / MPER / HIV-1 / membrane fusion / AIDS / Apoptosis / Cell membrane / Coiled coil / Envelope protein / Fusion protein / Host-virus interaction
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / Oxidative Stress Induced Senescence ...virus-mediated perturbation of host defense response => GO:0019049 / : / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / Oxidative Stress Induced Senescence / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Dectin-2 family / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / cellular response to amino acid starvation / host cell endosome membrane / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / clathrin-dependent endocytosis of virus by host cell / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / membrane => GO:0016020 / viral protein processing / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / chromatin binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Single helix bin / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like ...Single helix bin / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / General control transcription factor GCN4 / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, J. / Lu, M.
CitationJournal: Biochemistry / Year: 2009
Title: Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation.
Authors: Liu, J. / Deng, Y. / Dey, A. / Moore, J. / Lu, M.
History
DepositionFeb 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
B: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
C: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
D: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
E: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
F: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,91319
Polymers32,4926
Non-polymers1,42013
Water1,40578
1
A: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
B: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
C: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,33513
Polymers16,2463
Non-polymers1,08910
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-96 kcal/mol
Surface area8750 Å2
MethodPISA
2
D: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
E: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
F: Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5776
Polymers16,2463
Non-polymers3313
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-80 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.527, 48.157, 81.782
Angle α, β, γ (deg.)90.00, 95.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Fusion complex of HIV-1 Envelope glycoprotein and Saccharomyces cerevisiae General control protein GCN4


Mass: 5415.377 Da / Num. of mol.: 6
Fragment: C-terminal MPER of HIV-1 GP41, Leucine-zipper domain of GCN4
Mutation: L27K, N30I, Y31K, H32R, L33I, V37I, A38K, L40I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1, (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
References: UniProt: Q4QX39, UniProt: P03069, UniProt: P03377*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1M sodium HEPES, 0.1M ammonium dihydrogenphosphate, 50% MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→19.6 Å / Num. all: 22010 / Num. obs: 22010 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2171 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 2→19.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.784 / SU ML: 0.155
Isotropic thermal model: Isotropic with TLS groups assigned for each protein chain
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.202 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26908 1110 5 %RANDOM
Rwork0.21347 ---
all0.21636 22010 --
obs0.21636 22010 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å2-0.58 Å2
2--2.96 Å20 Å2
3----4 Å2
Refinement stepCycle: LAST / Resolution: 2→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 25 142 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222383
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9443215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7955238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85823.945109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90315494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.191512
X-RAY DIFFRACTIONr_chiral_restr0.1390.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021646
X-RAY DIFFRACTIONr_nbd_refined0.2370.21029
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.218
X-RAY DIFFRACTIONr_mcbond_it1.3841.51277
X-RAY DIFFRACTIONr_mcangle_it2.12521988
X-RAY DIFFRACTIONr_scbond_it3.44131418
X-RAY DIFFRACTIONr_scangle_it4.4464.51227
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 70 -
Rwork0.288 1472 -
obs-1542 96.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2163-1.39245.33543.6545-8.561230.8846-0.03890.00080.11210.235-0.2357-0.1787-0.75761.09790.2746-0.2518-0.11030.0318-0.1055-0.0219-0.13116.7025.71613.575
21.22320.11253.96631.4639-4.275331.2792-0.0282-0.1144-0.06440.04620.03620.0672-0.19520.083-0.008-0.32340.0773-0.0346-0.2293-0.0493-0.0916-0.561-1.74513.452
31.52830.1305-0.2223.1648-8.091223.5851-0.06640.082-0.18650.05210.25830.0510.71650.1741-0.1919-0.11860.158-0.0412-0.0802-0.1367-0.11999.52-4.36711.843
42.36622.2086.04396.523114.160934.3643-0.1790.09540.1698-0.4625-0.21490.2164-1.4664-0.46980.3939-0.22390.1134-0.0045-0.09710.0285-0.132-20.611.70612.303
51.3013-0.3867-2.595.29411.471732.73050.1539-0.0529-0.09580.2813-0.19060.08040.3249-0.38930.0367-0.2513-0.0209-0.0181-0.2660.0361-0.1101-15.4452.46315.546
61.57070.81390.93311.95455.40333.7861-0.01980.14840.1948-0.13720.2057-0.112-0.61480.4642-0.1859-0.24550.01890.0562-0.21390.0451-0.0456-10.00211.12212.143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 42
2X-RAY DIFFRACTION2B3 - 42
3X-RAY DIFFRACTION3C3 - 42
4X-RAY DIFFRACTION4D2 - 42
5X-RAY DIFFRACTION5E3 - 42
6X-RAY DIFFRACTION6F2 - 42

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