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- PDB-3msh: Crystal structure of Hepatitis B X-Interacting Protein at high re... -

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Basic information

Entry
Database: PDB / ID: 3msh
TitleCrystal structure of Hepatitis B X-Interacting Protein at high resolution
ComponentsHepatitis B virus X-interacting protein
KeywordsPROTEIN BINDING / alpha-beta proteins / profilin-like fold / Roadblock/LC7 domain superfamily
Function / homology
Function and homology information


positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to lysosome / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / Macroautophagy / regulation of cell size ...positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to lysosome / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / Macroautophagy / regulation of cell size / mTORC1-mediated signalling / positive regulation of TOR signaling / positive regulation of TORC1 signaling / viral genome replication / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein localization to nucleus / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / lysosome / lysosomal membrane / positive regulation of gene expression / protein-containing complex / cytosol
Similarity search - Function
Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR5 / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / PHOSPHATE ION / Ragulator complex protein LAMTOR5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsGarcia-Saez, I. / Skoufias, D.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Characterization of HBXIP: The Protein That Interacts with the Anti-Apoptotic Protein Survivin and the Oncogenic Viral Protein HBx.
Authors: Garcia-Saez, I. / Lacroix, F.B. / Blot, D. / Gabel, F. / Skoufias, D.A.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatitis B virus X-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2567
Polymers10,6941
Non-polymers5626
Water1,22568
1
A: Hepatitis B virus X-interacting protein
hetero molecules

A: Hepatitis B virus X-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,51114
Polymers21,3882
Non-polymers1,12312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3430 Å2
ΔGint-20 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.161, 49.161, 72.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hepatitis B virus X-interacting protein / HBV X-interacting protein / HBX-interacting protein


Mass: 10694.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBXIP, XIP / Plasmid: pET-23d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43504

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Non-polymers , 5 types, 74 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20-24% PEG3350, 20% isopropanol, 0.1M tri-sodium citrate dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2009
Details: Optics: Horizontally bended Ge(220). Mirrors: Vertically bended multilayer
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.51→40.63 Å / Num. all: 14364 / Num. obs: 14314 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 13.1 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.049 / Net I/σ(I): 11.4
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1994 / Rsym value: 0.65 / % possible all: 96.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MS6

3ms6


Resolution: 1.51→40.63 Å / SU ML: 0.18 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 1364 9.95 %
Rwork0.1802 --
obs0.1833 13713 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.24 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3052 Å2-0 Å20 Å2
2---0.3052 Å2-0 Å2
3---0.6103 Å2
Refinement stepCycle: LAST / Resolution: 1.51→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms660 0 36 68 764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006744
X-RAY DIFFRACTIONf_angle_d1.0461011
X-RAY DIFFRACTIONf_dihedral_angle_d18.17288
X-RAY DIFFRACTIONf_chiral_restr0.072123
X-RAY DIFFRACTIONf_plane_restr0.003129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.56690.26071140.23191061X-RAY DIFFRACTION83
1.5669-1.62970.21521260.18551140X-RAY DIFFRACTION91
1.6297-1.70380.21391340.18041173X-RAY DIFFRACTION93
1.7038-1.79370.23651350.17581213X-RAY DIFFRACTION95
1.7937-1.9060.21711330.17921242X-RAY DIFFRACTION96
1.906-2.05320.20061410.15881261X-RAY DIFFRACTION98
2.0532-2.25980.18341390.15511275X-RAY DIFFRACTION99
2.2598-2.58680.20461430.16971300X-RAY DIFFRACTION99
2.5868-3.25880.20871460.17911312X-RAY DIFFRACTION99
3.2588-40.630.21371530.18351372X-RAY DIFFRACTION97
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)
11.0816-0.3171-0.5451.55450.04291.3232-0.0114-0.0079-0.0407-0.1622-0.1088-0.06320.04780.01630.10410.1090.0023-0.00110.1227-0.01020.09924.124411.01187.1333
21.40251.45720.28871.97890.94240.9469-0.10920.5616-0.146-0.20470.2445-0.0885-0.027-0.0253-0.05480.2311-0.1753-0.01420.5156-0.19980.1897-11.288-1.55647.2715
31.6282-0.2067-1.3811.56720.37031.46550.17050.14420.06150.084-0.22930.0627-0.1271-0.38810.09270.1055-0.01870.00450.1484-0.02020.0803-2.919111.774213.2382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:54)
2X-RAY DIFFRACTION2(chain A and resid 55:63)
3X-RAY DIFFRACTION3(chain A and resid 64:89)

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