[English] 日本語
Yorodumi
- PDB-1bt6: P11 (S100A10), LIGAND OF ANNEXIN II IN COMPLEX WITH ANNEXIN II N-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bt6
TitleP11 (S100A10), LIGAND OF ANNEXIN II IN COMPLEX WITH ANNEXIN II N-TERMINUS
Components
  • ANNEXIN II
  • S100A10
KeywordsCOMPLEX (LIGAND/ANNEXIN) / S100 FAMILY / EF-HAND PROTEIN / COMPLEX (LIGAND-ANNEXIN) / LIGAND OF ANNEXIN II / CALCIUM/PHOSPHOLIPID BINDING PROTEIN / COMPLEX (LIGAND-ANNEXIN) complex
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of cytosolic calcium levels / Dissolution of Fibrin Clot / phospholipase inhibitor activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / endocardial cell differentiation / positive regulation of chondrocyte differentiation / growth plate cartilage development ...voltage-gated calcium channel activity involved in regulation of cytosolic calcium levels / Dissolution of Fibrin Clot / phospholipase inhibitor activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / endocardial cell differentiation / positive regulation of chondrocyte differentiation / growth plate cartilage development / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / vesicle budding from membrane / plasma membrane protein complex / calcium-dependent phospholipid binding / positive regulation of calcium ion transport / virion binding / Dissolution of Fibrin Clot / vesicle membrane / phosphatidylserine binding / positive regulation of transforming growth factor beta receptor signaling pathway / bone mineralization / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / positive regulation of focal adhesion assembly / calcium ion homeostasis / cytoskeletal protein binding / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / calcium channel complex / positive regulation of GTPase activity / Neutrophil degranulation / protein localization to plasma membrane / mRNA transcription by RNA polymerase II / calcium channel activity / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / : / vesicle / transmembrane transporter binding / calcium ion binding / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein S100-A10 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Protein S100-A10 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Protein S100-A10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRety, S. / Sopkova, J. / Renouard, M. / Osterloh, D. / Gerke, V. / Russo-Marie, F. / Lewit-Bentley, A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: The crystal structure of a complex of p11 with the annexin II N-terminal peptide.
Authors: Rety, S. / Sopkova, J. / Renouard, M. / Osterloh, D. / Gerke, V. / Tabaries, S. / Russo-Marie, F. / Lewit-Bentley, A.
History
DepositionSep 2, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S100A10
B: S100A10
C: ANNEXIN II
D: ANNEXIN II


Theoretical massNumber of molelcules
Total (without water)25,1454
Polymers25,1454
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-65 kcal/mol
Surface area10320 Å2
MethodPISA
2
A: S100A10
B: S100A10
C: ANNEXIN II
D: ANNEXIN II

A: S100A10
B: S100A10
C: ANNEXIN II
D: ANNEXIN II


Theoretical massNumber of molelcules
Total (without water)50,2918
Polymers50,2918
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area13470 Å2
ΔGint-136 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.600, 56.400, 64.300
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.457998, -0.053155, -0.887363), (-0.024374, -0.997085, 0.072307), (-0.888619, 0.054745, 0.455367)133.80363, 54.89459, 78.87959
2given(-0.506522, 0.042448, -0.861181), (-0.119007, -0.99267, 0.021068), (-0.853975, 0.113158, 0.507861)133.22804, 64.91576, 72.08719

-
Components

#1: Protein S100A10 / P11 / CALPACTIN LIGHT CHAIN


Mass: 11088.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET23A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60903
#2: Protein/peptide ANNEXIN II


Mass: 1483.706 Da / Num. of mol.: 2 / Fragment: N-TERMINAL
Source method: isolated from a genetically manipulated source
References: UniProt: P17785
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
250 mMTris-HCl11
31 mMdithiothreitol11
410 %PEG400012
510 %2-propanol12
6100 mMTris-HCl12

-
Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 1998 / Details: FOCUSSING MONOCHROMATOR AND MONOLAYER
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→62 Å / Num. obs: 9774 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 6.25 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 20.6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.96 / Rsym value: 0.61
Reflection
*PLUS
Num. measured all: 29481
Reflection shell
*PLUS
Rmerge(I) obs: 0.61

-
Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4P

1a4p


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.307 942 10 %RANDOM
Rwork0.228 ---
obs0.233 8511 96.8 %-
Displacement parametersBiso mean: 200.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 0 22 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0790.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it1.9762
X-RAY DIFFRACTIONp_mcangle_it3.1763
X-RAY DIFFRACTIONp_scbond_it3.263
X-RAY DIFFRACTIONp_scangle_it4.6354
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.2260.15
X-RAY DIFFRACTIONp_singtor_nbd0.3
X-RAY DIFFRACTIONp_multtor_nbd0.2430.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.3520.3
X-RAY DIFFRACTIONp_planar_tor3.72
X-RAY DIFFRACTIONp_staggered_tor24.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2620
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

+
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