[English] 日本語
Yorodumi
- PDB-5c7m: CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c7m
TitleCRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT
Components
  • E3 ubiquitin-protein ligase Itchy homolog
  • Polyubiquitin-C
KeywordsLIGASE/SIGNALING PROTEIN / LIGASE / UBIQUITIN-PROTEIN LIGASE / UBIQUITIN VARIANT / Structural Genomics Consortium / SGC / Structural Genomics / LIGASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / protein K29-linked ubiquitination / : / T cell anergy / positive regulation of T cell anergy / regulation of necroptotic process / CD4-positive, alpha-beta T cell proliferation ...regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / protein K29-linked ubiquitination / : / T cell anergy / positive regulation of T cell anergy / regulation of necroptotic process / CD4-positive, alpha-beta T cell proliferation / CXCR chemokine receptor binding / HECT-type E3 ubiquitin transferase / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / arrestin family protein binding / regulation of hematopoietic stem cell differentiation / negative regulation of type I interferon production / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / protein monoubiquitination / protein K63-linked ubiquitination / ligase activity / protein K48-linked ubiquitination / protein autoubiquitination / ribonucleoprotein complex binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / regulation of cell growth / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. ...E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / C2 domain / C2 domain profile. / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / E3 ubiquitin-protein ligase Itchy homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsWalker, J.R. / Hu, J. / Dong, A. / Wernimont, A. / Zhang, W. / Sidhu, S. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Cell / Year: 2016
Title: System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.
Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / ...Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / Sheng, Y. / Hao, Z. / Li, Y. / Brown, K.R. / Lemichez, E. / Chen, J. / Tong, Y. / Harper, J.W. / Moffat, J. / Rotin, D. / Schulman, B.A. / Sidhu, S.S.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Sep 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Itchy homolog
B: Polyubiquitin-C
C: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)66,5653
Polymers66,5653
Non-polymers00
Water543
1
A: E3 ubiquitin-protein ligase Itchy homolog
C: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)56,7972
Polymers56,7972
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area21980 Å2
MethodPISA
2
B: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)9,7681
Polymers9,7681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.115, 121.115, 85.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsAuthors have concluded that the biological assembly is dimeric. The interactions between chains A:B are likely to be due to crystal packing.

-
Components

#1: Protein E3 ubiquitin-protein ligase Itchy homolog / Itch / Atrophin-1-interacting protein 4 / AIP4 / NFE2-associated polypeptide 1 / NAPP1


Mass: 47028.676 Da / Num. of mol.: 1 / Fragment: HECT DOMAIN (UNP RESIDUES 524-899)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): V2R
References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Polyubiquitin-C


Mass: 9768.185 Da / Num. of mol.: 2 / Fragment: UNP residues 1-75
Mutation: Q2H, F3L, T9R, I44L, A46G, K48N, Q49K, T66N, H68Y, V70L, L73R, R74L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The ITCH and ubiquitin variant ubv.it.02 were mixed at molarity ratio 1:2, and then concentrated to 17mg/ml. The protein sample was mixed with 1mg/mL chymotrypsin at a 1:1000 (W/W) ...Details: The ITCH and ubiquitin variant ubv.it.02 were mixed at molarity ratio 1:2, and then concentrated to 17mg/ml. The protein sample was mixed with 1mg/mL chymotrypsin at a 1:1000 (W/W) chymotrypsin:protein ratio right before set up crystallization. Crystal was initially obtained from SGC-I screen condition A05. Crystal used for structure refinement was grown in 1.6M NH4SO4, 0.2M NaAc, 0.1M HEPES pH 7.5, 5% Ethylene Glycol in hanging drop setup, using 1.2uL protein, 1.2uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size for ~1 weeks. Harvested crystal was flash-frozen in liquid nitrogen. A well solution containing 20% glycerol was used as the cryo-protectant

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2013 / Details: ADSC Q315
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. obs: 14296 / % possible obs: 99.9 % / Redundancy: 18.1 % / Biso Wilson estimate: 104.49 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.02-3.0718.50.9086991.006100
3.07-3.1318.60.7576951.05100
3.13-3.1918.50.5996981.063100
3.19-3.2518.60.5117091.067100
3.25-3.3218.50.4027061.197100
3.32-3.418.50.337151.291100
3.4-3.4918.50.2526871.539100
3.49-3.5818.40.1997241.799100
3.58-3.6918.60.1737021.782100
3.69-3.818.40.1417111.877100
3.8-3.9418.40.1227032.143100
3.94-4.118.20.1047252.777100
4.1-4.2818.30.0927033.093100
4.28-4.5118.10.0797153.891100
4.51-4.7918.10.0767194.062100
4.79-5.1617.90.0777184.565100
5.16-5.6817.80.0777334.247100
5.68-6.517.40.0717204.759100
6.5-8.1916.80.0747426.504100
8.19-5015.80.06777220.72998.5

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
BALBESphasing
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TUG

3tug


Resolution: 3.03→49.43 Å / Cor.coef. Fo:Fc: 0.8905 / Cor.coef. Fo:Fc free: 0.8351 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.457
RfactorNum. reflection% reflectionSelection details
Rfree0.2969 583 4.08 %RANDOM
Rwork0.2537 ---
obs0.2554 14277 98.99 %-
Displacement parametersBiso mean: 103.68 Å2
Baniso -1Baniso -2Baniso -3
1-13.7063 Å20 Å20 Å2
2--13.7063 Å20 Å2
3----27.4126 Å2
Refinement stepCycle: LAST / Resolution: 3.03→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 0 3 3871
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087315HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8313081HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1492SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1182HARMONIC5
X-RAY DIFFRACTIONt_it7315HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion15.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion531SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7655SEMIHARMONIC4
LS refinement shellResolution: 3.03→3.27 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2737 130 4.62 %
Rwork0.2519 2683 -
all0.2531 2813 -
obs--96.06 %
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)
11.7606-0.3101-0.33881.8277-0.37260.57410.13050.07920.50120.04460.1781-0.2397-0.2004-0.1037-0.3086-0.02760.02920.1793-0.1407-0.0098-0.075-1.8681-36.572325.4298
24.3258-1.25271.92054.4768-2.23834.9407-0.00750.09950.0327-0.0222-0.07080.2687-0.0011-0.36320.0783-0.2899-0.0184-0.2076-0.1970.05560.2554-29.4241-52.824319.5979
3-0.1207-0.06043.69460.5716-1.14356.5487-0.05120.403-0.1229-0.31610.00270.19440.1255-0.14380.04840.05230.19230.050.18120.2044-0.2529-30.9236-26.434215.0683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

+
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