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- PDB-5yb4: Crystal structure of HP23LN36KR -

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Basic information

Entry
Database: PDB / ID: 5yb4
TitleCrystal structure of HP23LN36KR
Components
  • HP23L
  • N36KR
KeywordsVIRAL PROTEIN/INHIBITOR / 6-HB / HIV-1 / VIRAL PROTEIN-INHIBITOR complex
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: 2.5 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: N36KR
D: N36KR
F: N36KR
H: HP23L
G: HP23L
I: HP23L


Theoretical massNumber of molelcules
Total (without water)21,5146
Polymers21,5146
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-89 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.280, 51.280, 142.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide N36KR


Mass: 4170.907 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#2: Protein/peptide HP23L


Mass: 3000.415 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: (A12) 10%(w/v) PEG 8000, 1M HEPES, PH=7.5, 8%(v/v) Ethylene glycol 13 (B1) 8%(w/v) PEG 4000, 1M Sodium acetate PH=4.6

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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: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→35.15 Å / Num. obs: 7140 / % possible obs: 100 % / Redundancy: 12.4 % / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.15 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.3
RfactorNum. reflection% reflection
Rfree0.2666 338 4.74 %
Rwork0.1881 --
obs0.1916 7128 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 0 23 1503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071498
X-RAY DIFFRACTIONf_angle_d0.9022006
X-RAY DIFFRACTIONf_dihedral_angle_d18.912918
X-RAY DIFFRACTIONf_chiral_restr0.052226
X-RAY DIFFRACTIONf_plane_restr0.005243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5003-3.150.29991640.21163297
3.150.2531740.17953493
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)
12.10990.1071-0.13320.6355-0.1580.55770.1563-1.2762-0.5734-0.0723-0.1325-0.13990.0824-0.2374-0.08530.2564-0.1398-0.00950.51930.0240.42663.9947-17.117211.0736
22.07681.830.16561.57920.1615-0.01310.2853-0.04180.4338-0.1825-0.04010.29980.051-0.1476-0.03840.2528-0.04090.01560.42990.02990.270164.0439-10.27954.0685
32.4221.20491.1551.92410.02440.77740.3072-1.06021.04920.2986-0.06420.0986-0.0523-0.201-0.08160.2857-0.0392-0.00870.5348-0.15320.442764.504-7.378113.3907
48.42331.9088-0.18122.8717-0.44571.27490.4031-0.7658-0.30971.1210.12920.112-0.088-0.28550.1230.58980.07890.15540.9365-0.07410.42867.2865-11.118222.306
53.85211.29821.17462.2132-0.36092.26910.42680.5096-1.6966-0.4096-0.2269-0.49550.7227-0.1134-0.13290.4025-0.03280.05110.4349-0.07930.514467.3402-23.26824.0187
62.20010.255-0.58244.2859-1.07082.07940.2262-0.030.5621-0.0207-0.11570.5622-0.1275-0.0103-0.05550.2941-0.05920.01470.4194-0.01140.569267.8095-1.47662.0502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 35 through 70 )
2X-RAY DIFFRACTION2chain 'D' and (resid 35 through 70 )
3X-RAY DIFFRACTION3chain 'F' and (resid 36 through 70 )
4X-RAY DIFFRACTION4chain 'H' and (resid 115 through 136 )
5X-RAY DIFFRACTION5chain 'G' and (resid 116 through 136 )
6X-RAY DIFFRACTION6chain 'I' and (resid 114 through 136 )

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