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- PDB-7c3z: The structure of class II tumor suppressor protein H-REV107 -

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Basic information

Entry
Database: PDB / ID: 7c3z
TitleThe structure of class II tumor suppressor protein H-REV107
ComponentsHRAS-like suppressor 3
KeywordsHYDROLASE / H-REV107 / HREV107 type II tumor suppressor gene / retinoid-inducible gene 1
Function / homology
Function and homology information


membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity ...membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / peroxisome organization / N-acyltransferase activity / phospholipid biosynthetic process / phospholipase A2 activity / lens fiber cell differentiation / phospholipase A2 / peroxisomal membrane / triglyceride metabolic process / acyltransferase activity / localization / phospholipid metabolic process / lipid catabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrial membrane / response to bacterium / peroxisome / nuclear envelope / lysosome / lysosomal membrane / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Lecithin retinol acyltransferase / LRAT domain profile. / LRAT domain
Similarity search - Domain/homology
Phospholipase A and acyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.957 Å
AuthorsHan, C.W. / Jeong, M.S. / Jang, S.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1D1A1B07043701 Korea, Republic Of
CitationJournal: Cancers (Basel) / Year: 2020
Title: A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic KRAS Mutants.
Authors: Han, C.W. / Jeong, M.S. / Ha, S.C. / Jang, S.B.
History
DepositionMay 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
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
A: HRAS-like suppressor 3


Theoretical massNumber of molelcules
Total (without water)14,3391
Polymers14,3391
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6140 Å2
Unit cell
Length a, b, c (Å)42.935, 52.996, 62.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HRAS-like suppressor 3 / Phospholipase A and acyltransferase 3 / Adipose-specific phospholipase A2 / AdPLA / Group XVI ...Phospholipase A and acyltransferase 3 / Adipose-specific phospholipase A2 / AdPLA / Group XVI phospholipase A1/A2 / H-rev 107 protein homolog / HREV107-1 / HRAS-like suppressor 1 / HRSL3 / HREV107-3 / Renal carcinoma antigen NY-REN-65


Mass: 14339.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAAT3, HRASLS3, HREV107, PLA2G16 / Production host: Escherichia coli (E. coli)
References: UniProt: P53816, phospholipase A1, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: polyethylene glycol 3,350 and 0.2 M potassium nitrate at pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 10814 / % possible obs: 99.9 % / Redundancy: 14 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 36.9
Reflection shellResolution: 1.957→2.027 Å / Rmerge(I) obs: 0.218 / Num. unique obs: 2465

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOT

4dot


Resolution: 1.957→29.461 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.37
RfactorNum. reflection% reflection
Rfree0.2629 546 5.07 %
Rwork0.2343 --
obs0.2357 10763 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.957→29.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 0 56 895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008862
X-RAY DIFFRACTIONf_angle_d0.8891171
X-RAY DIFFRACTIONf_dihedral_angle_d3.84517
X-RAY DIFFRACTIONf_chiral_restr0.051124
X-RAY DIFFRACTIONf_plane_restr0.006152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.957-2.15350.27721320.20582465X-RAY DIFFRACTION99
2.1535-2.4650.29811360.22012519X-RAY DIFFRACTION100
2.465-3.10510.27571340.24432563X-RAY DIFFRACTION100
3.1051-29.4610.24441440.24022670X-RAY DIFFRACTION100

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