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- PDB-6jqk: Structure of C34M/N36 -

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Basic information

Entry
Database: PDB / ID: 6jqk
TitleStructure of C34M/N36
Components
  • C34M
  • N36
KeywordsVIRAL PROTEIN / HIV / envlope / T20
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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
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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsYu, D.W. / Qin, B.
CitationJournal: To Be Published
Title: Structure of C34M/N36
Authors: Yu, D.W. / Qin, B.
History
DepositionMar 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: N36
C: C34M


Theoretical massNumber of molelcules
Total (without water)8,3742
Polymers8,3742
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14 kcal/mol
Surface area5710 Å2
MethodPISA
2
N: N36
C: C34M

N: N36
C: C34M

N: N36
C: C34M


Theoretical massNumber of molelcules
Total (without water)25,1236
Polymers25,1236
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area12300 Å2
ΔGint-111 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.126, 46.126, 143.351
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11N-602-

HOH

21N-607-

HOH

31N-612-

HOH

41N-617-

HOH

51C-723-

HOH

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Components

#1: Protein/peptide N36


Mass: 4152.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#2: Protein/peptide C34M


Mass: 4221.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.75 Å3/Da / Density % sol: 29.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Sodium chloride,0.1 M BIS-TRIS pH 5.5,25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2018
RadiationMonochromator: SI(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.498→38.48 Å / Num. obs: 9811 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.96 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Net I/σ(I): 20.34
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.43 / Num. unique obs: 1561 / CC1/2: 0.967 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AIK

1aik


Resolution: 1.498→38.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.12
RfactorNum. reflection% reflection
Rfree0.2269 454 4.72 %
Rwork0.2054 --
obs0.2067 9623 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.498→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms593 0 0 41 634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006621
X-RAY DIFFRACTIONf_angle_d0.803845
X-RAY DIFFRACTIONf_dihedral_angle_d14.653228
X-RAY DIFFRACTIONf_chiral_restr0.06292
X-RAY DIFFRACTIONf_plane_restr0.004110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4981-1.71490.33321420.25482966X-RAY DIFFRACTION97
1.7149-2.16060.26731500.23573075X-RAY DIFFRACTION99
2.1606-38.49290.20641620.1913128X-RAY DIFFRACTION98

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