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- PDB-6r2g: Crystal structure of a single-chain protein mimetic of the gp41 N... -

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Basic information

Entry
Database: PDB / ID: 6r2g
TitleCrystal structure of a single-chain protein mimetic of the gp41 NHR trimer in complex with the synthetic CHR peptide C34
Components
  • Envelope glycoprotein gp160
  • Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41
KeywordsBIOSYNTHETIC PROTEIN / gp41 / HIV / coiled-coil
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 ...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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / 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
PHOSPHATE ION / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCamara-Artigas, A. / Conejero-Lara, F. / Jurado, S. / Cano-Munoz, M. / Morel, B.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-76640-R Spain
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
Citation
Journal: J.Mol.Biol. / Year: 2019
Title: Structural and Thermodynamic Analysis of HIV-1 Fusion Inhibition Using Small gp41 Mimetic Proteins.
Authors: Jurado, S. / Cano-Munoz, M. / Morel, B. / Standoli, S. / Santarossa, E. / Moog, C. / Schmidt, S. / Laumond, G. / Camara-Artigas, A. / Conejero-Lara, F.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41 with potential as anti-HIV-1 drugs.
Authors: Crespillo, S. / Camara-Artigas, A. / Casares, S. / Morel, B. / Cobos, E.S. / Mateo, P.L. / Mouz, N. / Martin, C.E. / Roger, M.G. / El Habib, R. / Su, B. / Moog, C. / Conejero-Lara, F.
History
DepositionMar 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: 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: Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41
C: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5473
Polymers25,4522
Non-polymers951
Water95553
1
A: Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2712
Polymers21,1761
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)4,2761
Polymers4,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.201, 69.664, 95.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41


Mass: 21176.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03377*PLUS
#2: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 4275.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)
Strain: isolate BRU/LAI / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: P03377
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.78 Å3/Da / Density % sol: 31.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 4000, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→19.85 Å / Num. obs: 15041 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.029 / Rrim(I) all: 0.066 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.945.21.10310140.6840.5281.226100
8.91-19.853.80.02116110.0110.02490.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R61

4r61


Resolution: 1.9→19.852 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.21 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 1408 5.12 %
Rwork0.1902 --
obs0.1923 27509 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 5 53 1540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121516
X-RAY DIFFRACTIONf_angle_d1.1622042
X-RAY DIFFRACTIONf_dihedral_angle_d2.562944
X-RAY DIFFRACTIONf_chiral_restr0.049235
X-RAY DIFFRACTIONf_plane_restr0.007267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.96790.39761440.33182620X-RAY DIFFRACTION100
1.9679-2.04660.29741610.28252572X-RAY DIFFRACTION99
2.0466-2.13970.26231310.23582648X-RAY DIFFRACTION100
2.1397-2.25230.30371490.21162637X-RAY DIFFRACTION100
2.2523-2.39320.23751520.19912568X-RAY DIFFRACTION99
2.3932-2.57760.23731260.18422636X-RAY DIFFRACTION99
2.5776-2.83640.25231300.19282626X-RAY DIFFRACTION100
2.8364-3.24530.25271150.19272614X-RAY DIFFRACTION99
3.2453-4.08280.20041600.15672597X-RAY DIFFRACTION99
4.0828-19.85270.19311400.17792583X-RAY DIFFRACTION98
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)
10.50770.0408-0.42110.6559-0.03690.2574-0.0495-0.0029-0.01810.0041-0.11570.0592-0.1948-0.16440.00080.3038-0.0020.00940.3332-0.03160.338427.008246.374650.5071
20.3549-0.3203-0.13250.16850.05390.0668-0.0238-0.05560.0301-0.014-0.01760.04030.0212-0.20120.00330.3211-0.06340.02370.3296-0.02920.308224.40439.723454.1042
30.4823-0.3047-0.01980.7497-0.15420.1772-0.0114-0.0036-0.07890.0796-0.00810.04030.3387-0.11350.00060.2656-0.01610.00530.284-0.01750.302131.638739.352253.0944
40.2395-0.19850.0236-0.1560.13340.1007-0.09210.1079-0.039-0.0447-0.0404-0.0784-0.20210.2488-0.00030.3497-0.0304-0.02730.3620.01650.352434.556146.366541.2664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 161 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 34 )

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