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- PDB-4wlp: Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex -

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Basic information

Entry
Database: PDB / ID: 4wlp
TitleCrystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex
Components
  • Nuclear factor related to kappa-B-binding protein
  • Ubiquitin carboxyl-terminal hydrolase isozyme L5
KeywordsPROTEIN BINDING / UCH37 NFRKB Proteasome INO80 DUB
Function / homology
Function and homology information


lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of DNA replication / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of DNA repair / regulation of proteasomal protein catabolic process / positive regulation of DNA repair / telomere maintenance / Downregulation of TGF-beta receptor signaling / DNA Damage Recognition in GG-NER / UCH proteinases / ubiquitin-dependent protein catabolic process / DNA recombination / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / chromatin remodeling / DNA repair / nucleolus / positive regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor related to kappa-B-binding protein / NFRKB winged helix-like domain / NFRKB winged helix-like domain superfamily / NFRKB Winged Helix-like / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. ...Nuclear factor related to kappa-B-binding protein / NFRKB winged helix-like domain / NFRKB winged helix-like domain superfamily / NFRKB Winged Helix-like / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Nuclear factor related to kappa-B-binding protein / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.102 Å
AuthorsHemmis, C.W. / Hill, C.P. / VanderLinden, R. / Whitby, F.G.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM059135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM082545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM098401 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM097452 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA042014 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR001209 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase.
Authors: VanderLinden, R.T. / Hemmis, C.W. / Schmitt, B. / Ndoja, A. / Whitby, F.G. / Robinson, H. / Cohen, R.E. / Yao, T. / Hill, C.P.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
B: Nuclear factor related to kappa-B-binding protein


Theoretical massNumber of molelcules
Total (without water)49,9552
Polymers49,9552
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-37 kcal/mol
Surface area22030 Å2
MethodPISA
2
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
B: Nuclear factor related to kappa-B-binding protein

A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
B: Nuclear factor related to kappa-B-binding protein


Theoretical massNumber of molelcules
Total (without water)99,9094
Polymers99,9094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area11510 Å2
ΔGint-90 kcal/mol
Surface area42060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.488, 95.488, 131.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L5 / UCH-L5 / Ubiquitin C-terminal hydrolase UCH37 / Ubiquitin thioesterase L5


Mass: 36303.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL5, UCH37, AD-019, CGI-70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1
#2: Protein Nuclear factor related to kappa-B-binding protein / DNA-binding protein R kappa-B / INO80 complex subunit G


Mass: 13651.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFRKB, INO80G / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P4R8

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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: 3.01 Å3/Da / Density % sol: 59.15 % / Description: tetragonal bipyramidal
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16-18% PEG3350, 100-300 mM Ammonium Citrate, 7.0 vapor diffusion hanging drop, 2:1 or 2:2 ratios protein to reservoir
PH range: 7 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: single wavelength
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.1→38.68 Å / Num. obs: 11634 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 94.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.038 / Net I/σ(I): 17.6 / Num. measured all: 149789 / Scaling rejects: 39
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.1-3.3212.91.51122655520550.7610.433100
8.77-38.68110.0283651159310.00698.8

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Processing

Software
NameVersionClassification
Blu-Ice0.1.26data collection
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.102→38.68 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1045 9 %Random selection
Rwork0.1932 10560 --
obs0.1999 11605 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.81 Å2 / Biso mean: 95.7925 Å2 / Biso min: 37.87 Å2
Refinement stepCycle: final / Resolution: 3.102→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 0 3352
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093420
X-RAY DIFFRACTIONf_angle_d1.1094606
X-RAY DIFFRACTIONf_chiral_restr0.041493
X-RAY DIFFRACTIONf_plane_restr0.004605
X-RAY DIFFRACTIONf_dihedral_angle_d17.5181296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1016-3.2650.29891460.253714661612
3.265-3.46940.3371450.239314791624
3.4694-3.73710.28991450.199314681613
3.7371-4.11280.27641480.187114871635
4.1128-4.7070.20331480.158915041652
4.707-5.9270.24951510.197315291680
5.927-38.68290.28641620.191816271789
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)
13.8709-0.51830.28934.1343-1.25143.1670.18670.33710.24050.1288-0.4327-0.3048-0.30230.50390.03970.4183-0.0597-0.01780.59830.10740.546119.947789.566459.4372
22.5663-0.9847-2.54532.23560.55632.8350.1334-0.1911-0.3606-0.0263-0.1997-0.3201-0.16240.59360.12330.524-0.0047-0.00630.77290.1040.709827.639984.345863.8523
32.82440.6922-0.8573.0806-1.41111.8863-0.16910.40360.00730.11460.2979-0.48070.2826-0.26020.20570.79680.0790.10250.8238-0.01450.690132.638260.769559.5085
45.51941.634-0.20843.909-0.47232.2608-0.40960.6684-1.5355-0.92280.0615-0.68161.40170.25760.07121.48880.25980.24660.99790.09751.11128.042650.76762.7428
53.72112.30741.2584.5621-2.26143.92190.0273-0.2066-0.37461.40720.1952-0.64220.3781.6472-0.18011.2910.3365-0.01960.99860.03380.872526.954761.67872.5594
60.8252-0.6363-0.06036.8418-1.6962.8222-0.0312-0.0596-0.25520.2070.130.40180.0877-0.0379-0.34040.6714-0.10790.05730.74210.03420.73495.109780.659175.3629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 147 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 254 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 321 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 40 through 93 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 94 through 117 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 118 through 153 )B0

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