[English] 日本語
Yorodumi
- PDB-2y1n: Structure of c-Cbl-ZAP-70 peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y1n
TitleStructure of c-Cbl-ZAP-70 peptide complex
Components
  • E3 UBIQUITIN-PROTEIN LIGASE
  • TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
KeywordsLIGASE/TRANSFERASE / LIGASE-TRANSFERASE COMPLEX / UBIQUITIN RING E3 LIGASE
Function / homology
Function and homology information


T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / beta selection / positive thymic T cell selection ...T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / beta selection / positive thymic T cell selection / positive regulation of alpha-beta T cell differentiation / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of T cell differentiation / Interleukin-6 signaling / mast cell degranulation / T cell receptor complex / response to starvation / response to testosterone / Translocation of ZAP-70 to Immunological synapse / negative regulation of epidermal growth factor receptor signaling pathway / B cell activation / TGF-beta receptor signaling activates SMADs / Generation of second messenger molecules / RHOH GTPase cycle / T cell differentiation / immunological synapse / protein monoubiquitination / protein autoubiquitination / Nuclear events stimulated by ALK signaling in cancer / ephrin receptor binding / T cell migration / cellular response to platelet-derived growth factor stimulus / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / positive regulation of calcium-mediated signaling / peptidyl-tyrosine phosphorylation / T cell activation / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / response to gamma radiation / non-membrane spanning protein tyrosine kinase activity / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / non-specific protein-tyrosine kinase / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / calcium-mediated signaling / Spry regulation of FGF signaling / Negative regulation of MET activity / Constitutive Signaling by EGFRvIII / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / positive regulation of receptor-mediated endocytosis / SH3 domain binding / male gonad development / protein polyubiquitination / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / T cell receptor signaling pathway / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / protein tyrosine kinase activity / ubiquitin-dependent protein catabolic process / response to ethanol / cellular response to hypoxia / adaptive immune response / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / protein ubiquitination / immune response / cilium / cadherin binding / membrane raft / focal adhesion / calcium ion binding / DNA damage response / symbiont entry into host cell / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / zinc ion binding / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. ...Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Prokaryotic RING finger family 4 / Adaptor protein Cbl, N-terminal domain superfamily / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / Transcription Elongation Factor S-II; Chain A / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / : / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Zinc finger RING-type profile. / SH2 domain / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Zinc finger, RING/FYVE/PHD-type / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL / Tyrosine-protein kinase ZAP-70
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsDou, H. / Sibbet, G.J. / Huang, D.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural Basis for Autoinhibition and Phosphorylation-Dependent Activation of C-Cbl.
Authors: Dou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T.
History
DepositionDec 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 1.3Dec 20, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE
B: TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
C: E3 UBIQUITIN-PROTEIN LIGASE
D: TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,88810
Polymers92,5464
Non-polymers3426
Water6,125340
1
C: E3 UBIQUITIN-PROTEIN LIGASE
D: TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4445
Polymers46,2732
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-21.3 kcal/mol
Surface area18450 Å2
MethodPISA
2
A: E3 UBIQUITIN-PROTEIN LIGASE
B: TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4445
Polymers46,2732
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21.4 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.570, 93.570, 189.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE / CBL C-CBL / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE / PROTO-ONCOGENE C-CBL / RING FINGER PROTEIN ...CBL C-CBL / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE / PROTO-ONCOGENE C-CBL / RING FINGER PROTEIN 55 / SIGNAL TRANSDUCTION PROTEIN CBL


Mass: 44928.695 Da / Num. of mol.: 2 / Fragment: RESIDUES 47-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE


Mass: 1344.275 Da / Num. of mol.: 2 / Fragment: PEPTIDE, RESIDUES 286-297 / Source method: obtained synthetically
Details: ZAP-70 PEPTIDE (TLNSDG(P)YTPEPA) WITH PHOSPHOTYROSINE AT POSITION 7
Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P43403, non-specific protein-tyrosine kinase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.83 % / Description: NONE
Crystal growDetails: 18-20% (W/V) PEG 3350, 0.2 M AMMONIUM FORMATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2010
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.395
ReflectionResolution: 2→50 Å / Num. obs: 63238 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBL

2cbl


Resolution: 1.999→45.423 Å / σ(F): 1.36 / Phase error: 30.1 / Stereochemistry target values: TWIN_LSQ_F
Details: RESIDUES OMITTED DUE TO POORLY DEFINED ELECTRON DENSITY. CHAIN A RESIDUES 355-361, CHAIN C RESIDUES 355-35 CHAINS B AND D RESIDUES 1-3. DUE TO POORLY DEFINED ELECTRON DENSITY, LYS53 AND ...Details: RESIDUES OMITTED DUE TO POORLY DEFINED ELECTRON DENSITY. CHAIN A RESIDUES 355-361, CHAIN C RESIDUES 355-35 CHAINS B AND D RESIDUES 1-3. DUE TO POORLY DEFINED ELECTRON DENSITY, LYS53 AND LYS54 IN CHAINS A AND C WERE BUILT AS ALANINES.
RfactorNum. reflection% reflection
Rfree0.1804 3219 5.1 %
Rwork0.1582 --
obs0.159 63238 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.127 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 39.82 Å2
Baniso -1Baniso -2Baniso -3
1-5.0461 Å20 Å20 Å2
2--5.0461 Å20 Å2
3----10.0922 Å2
Refinement stepCycle: LAST / Resolution: 1.999→45.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 6 340 6623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086434
X-RAY DIFFRACTIONf_angle_d1.1428695
X-RAY DIFFRACTIONf_dihedral_angle_d16.142406
X-RAY DIFFRACTIONf_chiral_restr0.069928
X-RAY DIFFRACTIONf_plane_restr0.0061114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9993-2.03380.27041620.26182978X-RAY DIFFRACTION94
2.0338-2.07070.26231700.25012961X-RAY DIFFRACTION94
2.0707-2.11060.2241620.23782997X-RAY DIFFRACTION95
2.1106-2.15360.24421500.21412984X-RAY DIFFRACTION95
2.1536-2.20040.23561570.20853002X-RAY DIFFRACTION95
2.2004-2.25160.23811650.21352997X-RAY DIFFRACTION95
2.2516-2.30790.22111770.21622970X-RAY DIFFRACTION94
2.3079-2.37030.2151530.20363010X-RAY DIFFRACTION95
2.3703-2.440.21541710.19452993X-RAY DIFFRACTION95
2.44-2.51870.22261480.19393031X-RAY DIFFRACTION95
2.5187-2.60870.20011660.19242986X-RAY DIFFRACTION95
2.6087-2.7130.21411600.18853001X-RAY DIFFRACTION95
2.713-2.83640.21921650.18263008X-RAY DIFFRACTION95
2.8364-2.98580.1961550.17542979X-RAY DIFFRACTION95
2.9858-3.17270.17921670.17063001X-RAY DIFFRACTION95
3.1727-3.41730.15921420.14613023X-RAY DIFFRACTION96
3.4173-3.76060.15191480.12913041X-RAY DIFFRACTION95
3.7606-4.30330.15691610.11163006X-RAY DIFFRACTION95
4.3033-5.41620.1341760.11122998X-RAY DIFFRACTION94
5.4162-29.44370.15031640.12843027X-RAY DIFFRACTION95

+
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