[English] 日本語
Yorodumi
- PDB-5a1k: Crystal structure of calcium-free human adseverin domains A1-A3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a1k
TitleCrystal structure of calcium-free human adseverin domains A1-A3
ComponentsADSEVERIN
KeywordsACTIN-BINDING PROTEIN / ACTIN
Function / homology
Function and homology information


positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of actin nucleation / positive regulation of megakaryocyte differentiation / sequestering of actin monomers / calcium-ion regulated exocytosis / actin filament severing / actin filament capping ...positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of actin nucleation / positive regulation of megakaryocyte differentiation / sequestering of actin monomers / calcium-ion regulated exocytosis / actin filament severing / actin filament capping / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / podosome / anchoring junction / phosphatidylserine binding / brush border / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / cell projection / actin filament binding / actin cytoskeleton / actin binding / cell cortex / positive regulation of apoptotic process / negative regulation of cell population proliferation / calcium ion binding / extracellular exosome / cytoplasm
Similarity search - Function
Gelsolin-like domain superfamily / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChumnarnsilpa, S. / Robinson, R.C. / Grimes, J.M. / Leyrat, C.
CitationJournal: Nat.Commun. / Year: 2015
Title: Calcium-Controlled Conformational Choreography in the N-Terminal Half of Adseverin.
Authors: Chumnarnsilpa, S. / Robinson, R.C. / Grimes, J.M. / Leyrat, C.
History
DepositionApr 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADSEVERIN
B: ADSEVERIN


Theoretical massNumber of molelcules
Total (without water)77,6002
Polymers77,6002
Non-polymers00
Water1,928107
1
A: ADSEVERIN


Theoretical massNumber of molelcules
Total (without water)38,8001
Polymers38,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADSEVERIN


Theoretical massNumber of molelcules
Total (without water)38,8001
Polymers38,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.410, 65.250, 105.190
Angle α, β, γ (deg.)90.00, 118.27, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.551, 0.834), (0.008, -1, -0.006), (0.834, 0.01, -0.551)
Vector: -25.024, -12.391, 46.356)

-
Components

#1: Protein ADSEVERIN / SCINDERIN


Mass: 38799.824 Da / Num. of mol.: 2 / Fragment: DOMAINS A1-A3, RESIDUES 6-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSY5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9Y6U3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.67 Å3/Da / Density % sol: 47.3 % / Description: NONE
Crystal growDetails: 20 % POLYETHYLENE GLYCOL 3350, 100 MM BIS-TRIS PROPANE PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0033
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0033 Å / Relative weight: 1
ReflectionResolution: 2.9→59.6 Å / Num. obs: 17766 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 5.5 % / Biso Wilson estimate: 79.21 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.5 / % possible all: 95

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D0N RESIDUES 27-370

1d0n


Resolution: 2.9→59.63 Å / Cor.coef. Fo:Fc: 0.8906 / Cor.coef. Fo:Fc free: 0.8939 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 904 5.09 %RANDOM
Rwork0.2396 ---
obs0.24 17745 97.76 %-
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.7867 Å20 Å2-4.5219 Å2
2--0.2475 Å20 Å2
3----4.0342 Å2
Refine analyzeLuzzati coordinate error obs: 0.499 Å
Refinement stepCycle: LAST / Resolution: 2.9→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 0 107 5521
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085527HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.127448HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1967SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes156HARMONIC2
X-RAY DIFFRACTIONt_gen_planes794HARMONIC5
X-RAY DIFFRACTIONt_it5527HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion25.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion683SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6076SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3332 155 5.5 %
Rwork0.3024 2663 -
all0.3041 2818 -
obs--97.76 %
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)
12.3365-0.0664-0.21450.5893-0.34880.8591-0.0004-0.00410.01750.00070.0013-0.018-0.0140.0399-0.0009-0.01290.0165-0.0008-0.01010.0073-0.0002-1.25975.195514.4076
21.6810.27620.18220.7865-0.50762.32650.0065-0.05510.00360.0275-0.0014-0.0153-0.0050.038-0.00510.0033-0.00680.00080.01080.0058-0.0066-13.4596-17.822137.3548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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