[English] 日本語
Yorodumi
- PDB-5l23: Crystal structure of the complex between the N-terminal SH3 domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l23
TitleCrystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand
Components
  • Adapter molecule crk
  • C3G derived peptide
KeywordsPROTEIN BINDING / SH3 / acetylation / amidation / Crkii / C3G
Function / homology
Function and homology information


PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / Downstream signal transduction ...PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / Downstream signal transduction / regulation of leukocyte migration / Rap protein signal transduction / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / regulation of dendrite development / p130Cas linkage to MAPK signaling for integrins / response to peptide / regulation of cell junction assembly / positive regulation of skeletal muscle acetylcholine-gated channel clustering / response to yeast / Regulation of signaling by CBL / nerve growth factor signaling pathway / negative regulation of wound healing / Regulation of actin dynamics for phagocytic cup formation / reelin-mediated signaling pathway / negative regulation of cell motility / VEGFA-VEGFR2 Pathway / establishment of endothelial barrier / negative regulation of natural killer cell mediated cytotoxicity / protein localization to membrane / MET activates RAP1 and RAC1 / regulation of GTPase activity / cellular response to insulin-like growth factor stimulus / Frs2-mediated activation / positive regulation of smooth muscle cell migration / enzyme-linked receptor protein signaling pathway / establishment of cell polarity / regulation of cell adhesion mediated by integrin / dendrite development / positive regulation of Rac protein signal transduction / ephrin receptor signaling pathway / RAC3 GTPase cycle / Erythropoietin activates RAS / cytoskeletal protein binding / cellular response to transforming growth factor beta stimulus / insulin-like growth factor receptor binding / cellular response to cAMP / signaling adaptor activity / ephrin receptor binding / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / positive regulation of GTPase activity / Downstream signal transduction / cellular response to nitric oxide / SH2 domain binding / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / guanyl-nucleotide exchange factor activity / hippocampus development / cell chemotaxis / regulation of actin cytoskeleton organization / Regulation of signaling by CBL / positive regulation of JNK cascade / cellular response to nerve growth factor stimulus / neuromuscular junction / cerebral cortex development / positive regulation of neuron projection development / response to hydrogen peroxide / SH3 domain binding / lipid metabolic process / neuron migration / nervous system development / actin cytoskeleton / signaling receptor complex adaptor activity / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / Ras protein signal transduction / early endosome / cell population proliferation / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / signal transduction / protein-containing complex / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Rap guanine nucleotide exchange factor 1 / Adapter molecule crk
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBhatt, V.S. / Krieger, I. / Sacchettini, J. / Cho, J.-H.
CitationJournal: To Be Published
Title: Crystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand
Authors: Bhatt, V.S. / Krieger, I. / Sacchettini, J. / Cho, J.-H.
History
DepositionJul 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adapter molecule crk
B: C3G derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9094
Polymers8,6972
Non-polymers2122
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-3 kcal/mol
Surface area4920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.600, 41.340, 56.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Adapter molecule crk / Proto-oncogene c-Crk / p38


Mass: 6971.731 Da / Num. of mol.: 1 / Fragment: UNP residues 134-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crk, Crko / Production host: Escherichia coli (E. coli) / References: UniProt: Q64010
#2: Protein/peptide C3G derived peptide


Mass: 1724.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q13905*PLUS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / Details: Lithium sulfate monohydrate, PEG 3350

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→33.43 Å / Num. obs: 6759 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.977 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.7
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.4 / CC1/2: 0.96 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cka

1cka


Resolution: 1.77→33.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21037 264 3.9 %RANDOM
Rwork0.17439 ---
obs0.17587 6462 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.77→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 11 99 726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02662
X-RAY DIFFRACTIONr_bond_other_d00.02616
X-RAY DIFFRACTIONr_angle_refined_deg2.6111.988892
X-RAY DIFFRACTIONr_angle_other_deg3.5563.0071434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.509577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06724.32437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64115113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.588156
X-RAY DIFFRACTIONr_chiral_restr0.1380.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021750
X-RAY DIFFRACTIONr_gen_planes_other0.0280.02148
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_it1.661.035303
X-RAY DIFFRACTIONr_mcbond_other1.5441.03302
X-RAY DIFFRACTIONr_mcangle_it2.561.52378
X-RAY DIFFRACTIONr_mcangle_other2.5641.523379
X-RAY DIFFRACTIONr_scbond_it2.7081.385359
X-RAY DIFFRACTIONr_scbond_other2.7081.385359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2041.934514
X-RAY DIFFRACTIONr_long_range_B_refined6.76910.73839
X-RAY DIFFRACTIONr_long_range_B_other6.78110.723839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.771→1.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 14 -
Rwork0.14 468 -
obs--99.79 %

+
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