[English] 日本語
Yorodumi
- PDB-2ak5: beta PIX-SH3 complexed with a Cbl-b peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ak5
Titlebeta PIX-SH3 complexed with a Cbl-b peptide
Components
  • 8-residue peptide from a signal transduction protein CBL-B
  • Rho guanine nucleotide exchange factor 7
KeywordsENDOCYTOSIS/EXOCYTOSIS / adaptor proteins / Cin85 / PIX/COOL / Cbl / protein-protein interaction / endocytosis / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / regulation of GTP binding / Ephrin signaling / EGFR downregulation / RHOU GTPase cycle / NRAGE signals death through JNK / RHOV GTPase cycle / peptidyl-amino acid modification / G alpha (12/13) signalling events ...presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / regulation of GTP binding / Ephrin signaling / EGFR downregulation / RHOU GTPase cycle / NRAGE signals death through JNK / RHOV GTPase cycle / peptidyl-amino acid modification / G alpha (12/13) signalling events / RHOJ GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / positive regulation of T cell anergy / postsynaptic actin cytoskeleton organization / astrocyte cell migration / positive regulation of growth hormone secretion / storage vacuole / CD4-positive, alpha-beta T cell proliferation / negative regulation of epidermal growth factor-activated receptor activity / negative regulation of CD4-positive, alpha-beta T cell proliferation / gamma-tubulin binding / NLS-bearing protein import into nucleus / lamellipodium assembly / negative regulation of T cell receptor signaling pathway / regulation of protein binding / Golgi organization / small GTPase mediated signal transduction / mitotic spindle pole / GABA-ergic synapse / regulation of GTPase activity / hematopoietic progenitor cell differentiation / ruffle / positive regulation of protein ubiquitination / guanyl-nucleotide exchange factor activity / phosphotyrosine residue binding / protein catabolic process / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / SH3 domain binding / ubiquitin protein ligase activity / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of GTPase activity / cell cortex / postsynapse / lamellipodium / growth cone / T cell receptor signaling pathway / positive regulation of protein binding / immune response / intracellular signal transduction / centrosome / neuron projection / positive regulation of apoptotic process / membrane raft / focal adhesion / neuronal cell body / calcium ion binding / protein kinase binding / signal transduction / protein-containing complex / zinc ion binding / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
betaPIX coiled coil / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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 ...betaPIX coiled coil / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / CBL proto-oncogene N-terminal domain 1 / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily / Dbl homology (DH) domain signature. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Variant SH3 domain / Ubiquitin associated domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain superfamily / RhoGEF domain / Dbl homology (DH) domain profile. / Dbl homology (DH) domain / Ubiquitin-associated domain (UBA) profile. / Ubiquitin-associated domain / SH3 Domains / Zinc finger RING-type signature. / Zinc finger, RING-type, conserved site / PH domain / Ring finger / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / SH3 type barrels. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain pair / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 7 / E3 ubiquitin-protein ligase CBL-B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJozic, D. / Cardenes, N. / Deribe, Y.L. / Moncalian, G. / Hoeller, D. / Groemping, Y. / Dikic, I. / Rittinger, K. / Bravo, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Cbl promotes clustering of endocytic adaptor proteins.
Authors: Jozic, D. / Cardenes, N. / Deribe, Y.L. / Moncalian, G. / Hoeller, D. / Groemping, Y. / Dikic, I. / Rittinger, K. / Bravo, J.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
D: 8-residue peptide from a signal transduction protein CBL-B


Theoretical massNumber of molelcules
Total (without water)15,5893
Polymers15,5893
Non-polymers00
Water2,954164
1
A: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
D: 8-residue peptide from a signal transduction protein CBL-B

A: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
D: 8-residue peptide from a signal transduction protein CBL-B


Theoretical massNumber of molelcules
Total (without water)31,1786
Polymers31,1786
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565x-y,-y+1,-z+1/31
Unit cell
Length a, b, c (Å)69.338, 69.338, 58.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Rho guanine nucleotide exchange factor 7 / PAK-interacting exchange factor beta / Beta-Pix


Mass: 7290.925 Da / Num. of mol.: 2 / Fragment: beta-pix SH3A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (unknown) / Strain (production host): BL21 DE3 / References: UniProt: O55043
#2: Protein/peptide 8-residue peptide from a signal transduction protein CBL-B


Mass: 1007.236 Da / Num. of mol.: 1 / Fragment: residues 904-911 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide can be naturally found in Homo sapiens (Human)Cbl-b
References: UniProt: Q13191
#3: Water ChemComp-HOH / water / SH3-binding protein CBL-B / RING finger protein 56 / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 291 K / pH: 6.5
Details: PEG 3000, SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 6.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1.5418
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→26.17 Å / Num. obs: 14106 / % possible obs: 99.5 % / Redundancy: 2.94 % / Rsym value: 0.086 / Net I/σ(I): 31.8
Reflection shellResolution: 1.85→1.93 Å / % possible all: 98.1

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SEM

1sem


Resolution: 1.85→26.17 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9263 / SU B: 9.0032 / SU ML: 0.1122 / Cross valid method: THROUGHOUT / ESU R: 0.3046 / ESU R Free: 0.1528
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -4.9993 %RANDOM
Rwork0.227 ---
obs0.2202 13340 99.5181 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-
2--0.04 Å2-
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 0 164 1216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d00.0211083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.8921465
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.053129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.315189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.070.2145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg00.02853
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.230.3496
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other0.180.5209
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.260.363
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.050.51
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

+
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