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- PDB-8z3t: Structure of P-98/N44 -

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Basic information

Entry
Database: PDB / ID: 8z3t
TitleStructure of P-98/N44
Components
  • Env polyprotein
  • P-98
KeywordsVIRAL PROTEIN / HIV / envlope / 6HB
Function / homology
Function and homology information


host cell endosome / clathrin-dependent endocytosis of virus by host cell / 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
Retroviral envelope protein / Retroviral envelope protein GP41-like
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLiu, N. / Qin, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of P-98/N44
Authors: Liu, N. / Qin, B.
History
DepositionApr 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Env polyprotein
B: Env polyprotein
C: Env polyprotein
D: P-98
E: P-98
F: P-98


Theoretical massNumber of molelcules
Total (without water)25,7226
Polymers25,7226
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-88 kcal/mol
Surface area12100 Å2
MethodPISA
2
A: Env polyprotein
F: P-98


Theoretical massNumber of molelcules
Total (without water)8,5742
Polymers8,5742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-10 kcal/mol
Surface area6220 Å2
MethodPISA
3
B: Env polyprotein
D: P-98


Theoretical massNumber of molelcules
Total (without water)8,5742
Polymers8,5742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-11 kcal/mol
Surface area6390 Å2
MethodPISA
4
C: Env polyprotein
E: P-98


Theoretical massNumber of molelcules
Total (without water)8,5742
Polymers8,5742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.915, 35.970, 107.113
Angle α, β, γ (deg.)90.00, 92.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Env polyprotein


Mass: 5035.892 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A0A1V0G0J3
#2: Protein/peptide P-98


Mass: 3538.045 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Lithium sulfate monohydrate, BIS-TRIS, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.008→31.22 Å / Num. obs: 16306 / % possible obs: 97.4 % / Redundancy: 5.817 % / CC1/2: 0.985 / Rmerge(I) obs: 0.213 / Net I/σ(I): 4.91
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 5.49 % / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 2602 / CC1/2: 0.434 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→31.22 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3162 1590 10.03 %
Rwork0.2478 --
obs0.2546 15847 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 0 132 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011762
X-RAY DIFFRACTIONf_angle_d1.0262346
X-RAY DIFFRACTIONf_dihedral_angle_d4.783218
X-RAY DIFFRACTIONf_chiral_restr0.041267
X-RAY DIFFRACTIONf_plane_restr0.006302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.070.40621340.36231209X-RAY DIFFRACTION94
2.07-2.150.4171480.3461315X-RAY DIFFRACTION99
2.15-2.230.34841510.30051306X-RAY DIFFRACTION99
2.23-2.330.29761440.26461287X-RAY DIFFRACTION99
2.33-2.460.3341540.26121292X-RAY DIFFRACTION98
2.46-2.610.34111350.24981326X-RAY DIFFRACTION98
2.61-2.810.29941450.24341307X-RAY DIFFRACTION99
2.81-3.10.33471490.25751282X-RAY DIFFRACTION97
3.1-3.540.30551370.2311324X-RAY DIFFRACTION98
3.54-4.460.30411410.19291321X-RAY DIFFRACTION97
4.46-31.220.27841520.24881288X-RAY DIFFRACTION93

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