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- PDB-5yb2: Crystal structure of LP-11/N44 -

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Basic information

Entry
Database: PDB / ID: 5yb2
TitleCrystal structure of LP-11/N44
Components
  • (Envelope glycoprotein) x 2
  • LP-11
KeywordsVIRAL PROTEIN / 6-HB / HIV-1
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / Env polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsZhang, X. / Wang, X. / He, Y.
CitationJournal: Front Cell Infect Microbiol / Year: 2018
Title: Structural Insights into the Mechanisms of Action of Short-Peptide HIV-1 Fusion Inhibitors Targeting the Gp41 Pocket
Authors: Zhang, X. / Zhu, Y. / Hu, H. / Zhang, S. / Wang, P. / Chong, H. / He, J. / Wang, X. / He, Y.
History
DepositionSep 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Envelope glycoprotein
D: Envelope glycoprotein
F: Envelope glycoprotein
H: LP-11
G: LP-11
I: LP-11
B: Envelope glycoprotein
A: Envelope glycoprotein
C: Envelope glycoprotein
K: LP-11
J: LP-11
L: LP-11
M: Envelope glycoprotein
P: LP-11


Theoretical massNumber of molelcules
Total (without water)71,18014
Polymers71,18014
Non-polymers00
Water00
1
E: Envelope glycoprotein
D: Envelope glycoprotein
F: Envelope glycoprotein
H: LP-11
G: LP-11
I: LP-11


Theoretical massNumber of molelcules
Total (without water)30,0806
Polymers30,0806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-93 kcal/mol
Surface area9720 Å2
MethodPISA
2
B: Envelope glycoprotein
A: Envelope glycoprotein
C: Envelope glycoprotein
K: LP-11
J: LP-11
L: LP-11


Theoretical massNumber of molelcules
Total (without water)30,0806
Polymers30,0806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-93 kcal/mol
Surface area9560 Å2
MethodPISA
3
M: Envelope glycoprotein
P: LP-11

M: Envelope glycoprotein
P: LP-11

M: Envelope glycoprotein
P: LP-11


Theoretical massNumber of molelcules
Total (without water)33,0626
Polymers33,0626
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9460 Å2
ΔGint-95 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.884, 110.884, 125.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Envelope glycoprotein


Mass: 8020.283 Da / Num. of mol.: 5 / Fragment: UNP residues 426-467 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q1HMR5, UniProt: P04578*PLUS
#2: Protein/peptide Envelope glycoprotein


Mass: 5037.884 Da / Num. of mol.: 2 / Fragment: UNP residues 27-70 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q1HMR5, UniProt: P04578*PLUS
#3: Protein/peptide
LP-11


Mass: 3000.415 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.8→27.72 Å / Num. obs: 5647 / % possible obs: 100 % / Redundancy: 5.7 % / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155-000refinement
HKL-2000V1.0data processing
HKL-2000V1.0data scaling
PHASER7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→27.72 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.3068 252 -
Rwork0.283 --
obs0.2841 5647 100 %
Refinement stepCycle: LAST / Resolution: 3.8→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 0 0 3495
LS refinement shellResolution: 3.8002→4.7846 Å /
RfactorNum. reflection
Rfree0.3879 99
Rwork0.3231 -
Refinement TLS params.Method: refined / Origin x: -28.4142 Å / Origin y: 72.9693 Å / Origin z: 7.0774 Å
111213212223313233
T1.3569 Å2-0.0193 Å20.0648 Å2-1.2773 Å2-0.0324 Å2--1.1955 Å2
L1.9287 °2-0.6054 °20.4838 °2-2.0145 °20.1244 °2--1.3725 °2
S0.0827 Å °-0.0488 Å °-0.0474 Å °0.1322 Å °-0.2432 Å °0.2232 Å °-0.2695 Å °-0.3073 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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