[English] 日本語
Yorodumi
- PDB-3tca: Crystal structure of the Ras-associating and pleckstrin-homology ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tca
TitleCrystal structure of the Ras-associating and pleckstrin-homology domains of RIAM
ComponentsAmyloid beta A4 precursor protein-binding family B member 1-interacting protein
KeywordsSIGNALING PROTEIN / RA DOMAIN / RBD / PH DOMAIN / RAP1-INTERACTING ADAPTOR MOLECULE / INTEGRIN SIGNALING
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / T cell receptor complex / positive regulation of cell adhesion / lamellipodium / cytoskeleton / focal adhesion ...GRB2:SOS provides linkage to MAPK signaling for Integrins / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / T cell receptor complex / positive regulation of cell adhesion / lamellipodium / cytoskeleton / focal adhesion / signal transduction / plasma membrane / cytosol
Similarity search - Function
GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWu, J. / Hubbard, S.R.
CitationJournal: J.Cell Biol. / Year: 2012
Title: Rap1-interacting adapter molecule (RIAM) associates with the plasma membrane via a proximity detector.
Authors: Wynne, J.P. / Wu, J. / Su, W. / Mor, A. / Patsoukis, N. / Boussiotis, V.A. / Hubbard, S.R. / Philips, M.R.
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
B: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein


Theoretical massNumber of molelcules
Total (without water)68,6532
Polymers68,6532
Non-polymers00
Water4,306239
1
A: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein


Theoretical massNumber of molelcules
Total (without water)34,3261
Polymers34,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein


Theoretical massNumber of molelcules
Total (without water)34,3261
Polymers34,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.860, 82.389, 83.404
Angle α, β, γ (deg.)90.00, 95.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Amyloid beta A4 precursor protein-binding family B member 1-interacting protein / APBB1-interacting protein 1 / Proline-rich EVH1 ligand 1 / PREL-1 / Proline-rich protein 48


Mass: 34326.422 Da / Num. of mol.: 2
Fragment: Ras-associating and PH domain, UNP residues 150-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apbb1ip, Prel1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R5A3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 298 K / pH: 7
Details: 12% PEG3350, 100 mM LiAc, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 22885 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 19
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.291 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HK0

3hk0


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.885 / SU B: 17.53 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1222 5.1 %RANDOM
Rwork0.234 ---
obs0.236 22885 91.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.3 Å2
2---2.33 Å20 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3995 0 0 239 4234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.9535514
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5755487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80224.271199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06515730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.761522
X-RAY DIFFRACTIONr_chiral_restr0.060.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023078
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_it0.2131.52449
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.39823941
X-RAY DIFFRACTIONr_scbond_it0.41531632
X-RAY DIFFRACTIONr_scangle_it0.7214.51573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 91 -
Rwork0.28 1782 -
obs--97.4 %
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)
10.6349-0.07860.04141.24480.19150.49590.0564-0.02290.0204-0.0545-0.0236-0.03660.01850.0151-0.03280.0544-0.00770.02030.04540.01590.020616.07160.761237.5512
20.63510.3652-0.02311.63240.0530.27580.04870.03230.010.137-0.00820.00670.01620.0161-0.04060.03880.0089-0.01650.04490.01780.030619.80550.0443.8057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A178 - 437
2X-RAY DIFFRACTION2B179 - 437

+
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://pdbjlvh1.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