[English] 日本語
Yorodumi
- PDB-2xqn: Complex of the 2nd and 3rd LIM domains of TES with the EVH1 DOMAI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xqn
TitleComplex of the 2nd and 3rd LIM domains of TES with the EVH1 DOMAIN of MENA and the N-Terminal domain of actin-like protein Arp7A
Components
  • ACTIN-LIKE PROTEIN 7A
  • ENABLED HOMOLOG
  • TESTIN
KeywordsMETAL BINDING PROTEIN / METAL-BINDING PROTEIN / CYTOSKELETON / FOCAL ADHESION / ACROSOME
Function / homology
Function and homology information


actin polymerization-dependent cell motility / acrosome assembly / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / motile cilium / WW domain binding / Generation of second messenger molecules / single fertilization / acrosomal vesicle ...actin polymerization-dependent cell motility / acrosome assembly / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / motile cilium / WW domain binding / Generation of second messenger molecules / single fertilization / acrosomal vesicle / filopodium / male germ cell nucleus / axon guidance / structural constituent of cytoskeleton / SH3 domain binding / cell junction / lamellipodium / actin binding / cytoskeleton / cadherin binding / negative regulation of cell population proliferation / focal adhesion / synapse / Golgi apparatus / protein-containing complex / RNA binding / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Actin-like protein 7A, N-terminal / Actin-like protein 7A N-terminus / PET domain / PET testin / Testin, LIM domain 1 / Testin, LIM domain 2 / Testin, LIM domain 3 / : / PET Domain / PET domain profile. ...Actin-like protein 7A, N-terminal / Actin-like protein 7A N-terminus / PET domain / PET testin / Testin, LIM domain 1 / Testin, LIM domain 2 / Testin, LIM domain 3 / : / PET Domain / PET domain profile. / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / Cysteine Rich Protein / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Ribbon / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein enabled homolog / Testin / Actin-like protein 7A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsKnowles, P.P. / Briggs, D.C. / Murray-Rust, J. / McDonald, N.Q.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Molecular recognition of the Tes LIM2-3 domains by the actin-related protein Arp7A.
Authors: Boeda, B. / Knowles, P.P. / Briggs, D.C. / Murray-Rust, J. / Soriano, E. / Garvalov, B.K. / McDonald, N.Q. / Way, M.
History
DepositionSep 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Other ...Database references / Other / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Dec 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_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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACTIN-LIKE PROTEIN 7A
M: ENABLED HOMOLOG
T: TESTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0578
Polymers34,7303
Non-polymers3275
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-24.7 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.829, 86.791, 115.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ACTIN-LIKE PROTEIN 7A / ARP7A / ACTIN-LIKE-7-ALPHA


Mass: 7015.960 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FB810 / References: UniProt: Q9Y615
#2: Protein ENABLED HOMOLOG / MENA


Mass: 13343.019 Da / Num. of mol.: 1 / Fragment: EVH1 DOMAIN, RESIDUES 1-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FB810 / References: UniProt: Q8N8S7
#3: Protein TESTIN / TESS


Mass: 14370.611 Da / Num. of mol.: 1 / Fragment: LIM DOMAINS 2 AND 3, RESIDUES 296-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FB810 / References: UniProt: Q9UGI8
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.96 Å3/Da / Density % sol: 58.54 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: PROTEIN: 37.5 MG/ML OF PROTEIN COMPLEX IN 20MM TRIS-HCL PH 8.0, 100MM NACL RESERVOIR: 17.5 PEG 8K, 0.1MTRIS PH 8.5, 0.15M KSCN SITTING DROPS 2:1 PROTEIN:RESERVOIR, 22 DEG C CRYOPROTECTANT: N-PARATONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 17, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25.74 Å / Num. obs: 12008 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 79.7

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IYB

2iyb


Resolution: 2.62→25.56 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 11.816 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.477 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26811 565 4.7 %RANDOM
Rwork0.21525 ---
obs0.21776 11400 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.715 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2--4.2 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.62→25.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 5 49 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9142841
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.975262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62124.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02415339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5251510
X-RAY DIFFRACTIONr_chiral_restr0.1390.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211600
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_it0.8051.51310
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55722104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.243796
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7154.5736
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.618→2.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 35 -
Rwork0.338 786 -
obs--95.02 %

+
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