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- PDB-4m5x: Crystal structure of the USP7/HAUSP catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4m5x
TitleCrystal structure of the USP7/HAUSP catalytic domain
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / Ubiquitin-specific cysteine protease
Function / homology
Function and homology information


regulation of telomere capping / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / protein deubiquitination / negative regulation of gluconeogenesis / transcription-coupled nucleotide-excision repair / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / regulation of circadian rhythm / PML body / regulation of protein stability / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / p53 binding / rhythmic process / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / protein ubiquitination / protein stabilization / nuclear body / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. ...ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Single Sheet / Papain-like cysteine peptidase superfamily / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.187 Å
AuthorsMesecar, A.D. / Molland, K.L. / Zhou, Q.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: A 2.2 angstrom resolution structure of the USP7 catalytic domain in a new space group elaborates upon structural rearrangements resulting from ubiquitin binding.
Authors: Molland, K. / Zhou, Q. / Mesecar, A.D.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5375
Polymers82,2972
Non-polymers2403
Water4,450247
1
A: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3083
Polymers41,1481
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2282
Polymers41,1481
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.951, 67.579, 76.805
Angle α, β, γ (deg.)90.00, 96.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / USP7 / HAUSP / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / ...USP7 / HAUSP / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 41148.473 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 207-560)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 22% PEG3350, 0.2 M sodium bromide, 0.15 mM Cymal-7, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.187→76.354 Å / Num. all: 39518 / Num. obs: 38925 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 32.63 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.44
Reflection shellResolution: 2.187→2.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.9 / % possible all: 89

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NB8

1nb8


Resolution: 2.187→38.177 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.35 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1956 5.03 %
Rwork0.1799 --
obs0.1821 38887 98.17 %
all-39517 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.3125 Å2
Refinement stepCycle: LAST / Resolution: 2.187→38.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5496 0 3 247 5746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085612
X-RAY DIFFRACTIONf_angle_d1.1617564
X-RAY DIFFRACTIONf_dihedral_angle_d15.7482128
X-RAY DIFFRACTIONf_chiral_restr0.084807
X-RAY DIFFRACTIONf_plane_restr0.004987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1874-2.24210.26321270.2172337X-RAY DIFFRACTION89
2.2421-2.30270.23241470.19832662X-RAY DIFFRACTION100
2.3027-2.37040.25261410.18892653X-RAY DIFFRACTION100
2.3704-2.44690.27411620.1932677X-RAY DIFFRACTION100
2.4469-2.53440.27231190.19152685X-RAY DIFFRACTION100
2.5344-2.63580.24411450.18352683X-RAY DIFFRACTION100
2.6358-2.75570.26281310.17812684X-RAY DIFFRACTION100
2.7557-2.9010.23491270.1792690X-RAY DIFFRACTION100
2.901-3.08260.20791480.18312675X-RAY DIFFRACTION100
3.0826-3.32050.23381230.17222657X-RAY DIFFRACTION99
3.3205-3.65450.20361440.17112670X-RAY DIFFRACTION98
3.6545-4.18270.20751420.16062625X-RAY DIFFRACTION97
4.1827-5.26760.17351530.16522604X-RAY DIFFRACTION97
5.2676-38.1830.24461470.2062629X-RAY DIFFRACTION95
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)
12.59860.08440.69051.4188-0.31453.29630.03790.2273-0.33650.124-0.06120.09080.4643-0.23950.02550.3005-0.04580.02040.2679-0.08050.20120.68538.8374-36.3506
21.8813-1.3043-0.5821.3727-0.32740.64760.03310.17580.10140.1358-0.0785-0.4590.07330.10170.02410.2275-0.0119-0.0260.2955-0.01740.344650.198543.8093-40.8877
33.66690.4286-0.01273.22760.06871.85840.06050.01890.11540.2393-0.0743-0.02480.0418-0.0757-0.00740.16160.005-0.01680.1962-0.02210.12827.697551.451-37.8975
42.34170.1901-0.08871.47940.68063.2197-0.0707-0.0352-0.23270.27550.02810.11140.3994-0.23040.01520.239-0.02490.05040.1450.01710.186353.773971.58272.8377
51.606-0.1664-0.41951.80130.39730.4318-0.0613-0.13840.02480.1880.1048-0.39870.10940.2084-0.05590.22290.0118-0.02940.19270.01170.242980.249279.27960.5646
63.24631.039-0.61222.6032-0.34810.9871-0.0330.09410.18690.01820.06940.1479-0.0416-0.1474-0.02990.14790.0407-0.01730.15110.03250.147756.997682.9084-1.7162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 209 through 309 )
2X-RAY DIFFRACTION2chain 'A' and (resid 310 through 400 )
3X-RAY DIFFRACTION3chain 'A' and (resid 401 through 554 )
4X-RAY DIFFRACTION4chain 'B' and (resid 208 through 309 )
5X-RAY DIFFRACTION5chain 'B' and (resid 310 through 436 )
6X-RAY DIFFRACTION6chain 'B' and (resid 437 through 554 )

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