[English] 日本語
Yorodumi
- PDB-2vhf: Structure of the CYLD USP domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vhf
TitleStructure of the CYLD USP domain
ComponentsUBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD
KeywordsHYDROLASE / CYTOKINE SIGNALLING / LINKAGE SPECIFICITY / DEUBIQUITINATING ENZYME / LYS63- LINKED / ANTI-ONCOGENE / THIOL PROTEASE / CELL SIGNALLING / PHOSPHORYLATION / ZN-BINDING DOMAIN / UBIQUITIN / CELL CYCLE / USP DOMAIN / CROSS-BRACE / NF-KB / B-BOX / PROTEASE / CYTOPLASM / ALTERNATIVE SPLICING / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / regulation of cilium assembly / negative regulation of p38MAPK cascade / regulation of necroptotic process ...negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / regulation of cilium assembly / negative regulation of p38MAPK cascade / regulation of necroptotic process / ciliary tip / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / regulation of tumor necrosis factor-mediated signaling pathway / proline-rich region binding / K48-linked deubiquitinase activity / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of non-canonical NF-kappaB signal transduction / protein K63-linked deubiquitination / TNFR1-induced proapoptotic signaling / negative regulation of JNK cascade / positive regulation of T cell differentiation / negative regulation of type I interferon production / K63-linked deubiquitinase activity / negative regulation of NF-kappaB transcription factor activity / positive regulation of T cell receptor signaling pathway / necroptotic process / homeostasis of number of cells / protein deubiquitination / positive regulation of protein localization / negative regulation of canonical NF-kappaB signal transduction / TNFR1-induced NF-kappa-B signaling pathway / regulation of microtubule cytoskeleton organization / Negative regulators of DDX58/IFIH1 signaling / regulation of mitotic cell cycle / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / negative regulation of canonical Wnt signaling pathway / negative regulation of inflammatory response / centriolar satellite / spindle / Wnt signaling pathway / regulation of inflammatory response / microtubule / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / ciliary basal body / innate immune response / centrosome / protein kinase binding / perinuclear region of cytoplasm / proteolysis / zinc ion binding / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Phosphorylation region of CYLD, unstructured / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase ...Phosphorylation region of CYLD, unstructured / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / 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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase CYLD
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKomander, D. / Lord, C.J. / Scheel, H. / Swift, S. / Hofmann, K. / Ashworth, A. / Barford, D.
CitationJournal: Mol.Cell.Biol. / Year: 2008
Title: The Structure of the Cyld Usp Domain Explains its Specificity for Lys63-Linked Polyubiquitin and Reveals a B-Box Module
Authors: Komander, D. / Lord, C.J. / Scheel, H. / Swift, S. / Hofmann, K. / Ashworth, A. / Barford, D.
History
DepositionNov 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD
B: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9526
Polymers86,6902
Non-polymers2624
Water25214
1
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4763
Polymers43,3451
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4763
Polymers43,3451
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.494, 89.083, 171.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD / UBIQUITIN THIOESTERASE CYLD / UBIQUITIN-SPECIFIC -PROCESSING PROTEASE CYLD / DEUBIQUITINATING ...UBIQUITIN THIOESTERASE CYLD / UBIQUITIN-SPECIFIC -PROCESSING PROTEASE CYLD / DEUBIQUITINATING ENZYME CYLD / CYLD


Mass: 43345.180 Da / Num. of mol.: 2 / Fragment: USP DEUBIQUITINASE DOMAIN, RESIDUES 583-956
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NQC7, EC: 3.1.2.15
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.5-2% PEG 20000, 0.1 M MES [PH6.3], pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.04
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 23405 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 58.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDEphasing
HKL2Mapphasing
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.8→29.79 Å / SU ML: 0.53 / Cross valid method: PHENIX DEFAULT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFINED WITH PHENIX 1.3B DISORDERED SIDECHAINS WERE REFINED WITH OCCU 0.01 OR MUTATED TO ALA. ANISO RECORDS ARE CREATED BY TLS REFINEMENT IN PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1412 3.3 %RANDOM
Rwork0.233 ---
obs0.235 43133 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1--14.9842 Å2-0 Å20 Å2
2---5.8771 Å2-0 Å2
3---20.8613 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5247 0 4 14 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.00805360
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0937.4237262
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.4042 178
Rwork0.3102 4198
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)
10.89630.2902-0.50090.01690.140.31840.0541-0.02610.1235-0.0274-0.02950.006-0.04980.0102-0.03110.26980.02420.03190.2362-0.02680.266521.723662.579240.9863
20.2258-0.155-0.07030.8711-0.55130.8739-0.0639-0.01320.0027-0.06590.0452-0.00270.0609-0.09710.0290.2398-0.0094-0.02260.18380.08570.2787.88648.33036.1313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A583 - 956
2X-RAY DIFFRACTION2B583 - 956

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more