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- PDB-5jtv: USP7CD-UBL45 in complex with Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5jtv
TitleUSP7CD-UBL45 in complex with Ubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7 / HAUSP / C-terminal activation
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 / : / K48-linked deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...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 / : / K48-linked deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / : / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / negative regulation of gluconeogenesis / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of TORC1 signaling / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of signal transduction by p53 class mediator / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / positive regulation of protein ubiquitination / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / TNFR2 non-canonical NF-kB pathway
Similarity search - Function
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 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. / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.312 Å
AuthorsMurray, J.M. / Rouge, L.
CitationJournal: Structure / Year: 2016
Title: Molecular Understanding of USP7 Substrate Recognition and C-Terminal Activation.
Authors: Rouge, L. / Bainbridge, T.W. / Kwok, M. / Tong, R. / Di Lello, P. / Wertz, I.E. / Maurer, T. / Ernst, J.A. / Murray, J.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Polyubiquitin-B
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Polyubiquitin-B
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Polyubiquitin-B
G: Ubiquitin carboxyl-terminal hydrolase 7
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)310,6378
Polymers310,6378
Non-polymers00
Water00
1
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)77,6592
Polymers77,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-5 kcal/mol
Surface area32980 Å2
MethodPISA
2
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)77,6592
Polymers77,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-6 kcal/mol
Surface area32510 Å2
MethodPISA
3
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)77,6592
Polymers77,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-6 kcal/mol
Surface area32400 Å2
MethodPISA
4
G: Ubiquitin carboxyl-terminal hydrolase 7
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)77,6592
Polymers77,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-6 kcal/mol
Surface area32210 Å2
MethodPISA
5
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)155,3184
Polymers155,3184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-37 kcal/mol
Surface area59890 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28780 Å2
ΔGint-80 kcal/mol
Surface area115110 Å2
MethodPISA
7
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Polyubiquitin-B
G: Ubiquitin carboxyl-terminal hydrolase 7
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)155,3184
Polymers155,3184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-39 kcal/mol
Surface area59530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.611, 115.520, 257.822
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
Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 69082.352 Da / Num. of mol.: 4
Fragment: UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
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: Protein
Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.273→46.954 Å / Num. obs: 52986 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 100.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.055 / Rrim(I) all: 0.139 / Net I/σ(I): 11.4 / Num. measured all: 323509
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.273-3.2846.30.853199.6
15.182-115.4550.036198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2210refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nbf

1nbf


Resolution: 3.312→46.954 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 2594 5.09 %
Rwork0.2386 --
obs0.2402 50930 99.37 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.312→46.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20520 0 0 0 20520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420943
X-RAY DIFFRACTIONf_angle_d0.80828263
X-RAY DIFFRACTIONf_dihedral_angle_d15.49712707
X-RAY DIFFRACTIONf_chiral_restr0.0483077
X-RAY DIFFRACTIONf_plane_restr0.0053694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3124-3.37270.38661320.32122293X-RAY DIFFRACTION92
3.3727-3.43750.35581290.32292539X-RAY DIFFRACTION100
3.4375-3.50770.37941380.31732494X-RAY DIFFRACTION100
3.5077-3.58390.33441420.29822492X-RAY DIFFRACTION100
3.5839-3.66720.32941570.29782519X-RAY DIFFRACTION100
3.6672-3.75890.3681330.2972525X-RAY DIFFRACTION100
3.7589-3.86050.36271500.3022521X-RAY DIFFRACTION100
3.8605-3.9740.36571250.2772524X-RAY DIFFRACTION100
3.974-4.10220.34011460.25442529X-RAY DIFFRACTION100
4.1022-4.24880.28371310.24842536X-RAY DIFFRACTION100
4.2488-4.41880.26741340.23742543X-RAY DIFFRACTION100
4.4188-4.61970.26521320.22422583X-RAY DIFFRACTION100
4.6197-4.8630.261120.22032563X-RAY DIFFRACTION100
4.863-5.16730.23261300.21762566X-RAY DIFFRACTION100
5.1673-5.56570.27561280.23372567X-RAY DIFFRACTION100
5.5657-6.12480.26111640.25272564X-RAY DIFFRACTION100
6.1248-7.00850.30051220.25052626X-RAY DIFFRACTION100
7.0085-8.82040.22811500.21822624X-RAY DIFFRACTION100
8.8204-46.95920.18251390.18672728X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -33.298 Å / Origin y: 3.8899 Å / Origin z: 32.2674 Å
111213212223313233
T1.0941 Å20.0708 Å2-0.0968 Å2-1.1306 Å2-0.1244 Å2--1.1583 Å2
L0.423 °20.0285 °20.0674 °2-0.6102 °20.2175 °2--0.9121 °2
S-0.0635 Å °0.0714 Å °-0.001 Å °-0.0117 Å °-0.0995 Å °0.1305 Å °-0.1806 Å °-0.1951 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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