[English] 日本語
Yorodumi
- PDB-1avc: BOVINE ANNEXIN VI (CALCIUM-BOUND) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1avc
TitleBOVINE ANNEXIN VI (CALCIUM-BOUND)
ComponentsANNEXIN VI
KeywordsCALCIUM/PHOSPHOLIPID-BINDING PROTEIN / ANNEXIN / CALCIUM-BINDING / MEMBRANE-BINDING / CALCIUM-PHOSPHOLIPID-BINDING PROTEIN complex
Function / homology
Function and homology information


negative regulation of sequestering of calcium ion / growth plate cartilage chondrocyte differentiation / biomineral tissue development / chondroitin sulfate binding / mitochondrial calcium ion homeostasis / chromaffin granule membrane / regulation of muscle contraction / calcium-dependent phospholipid binding / calcium ion import / vesicle membrane ...negative regulation of sequestering of calcium ion / growth plate cartilage chondrocyte differentiation / biomineral tissue development / chondroitin sulfate binding / mitochondrial calcium ion homeostasis / chromaffin granule membrane / regulation of muscle contraction / calcium-dependent phospholipid binding / calcium ion import / vesicle membrane / cargo receptor activity / phosphatidylserine binding / mitochondrial crista / stress fiber / apoptotic signaling pathway / sarcolemma / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / calcium-dependent protein binding / actin filament binding / melanosome / heparin binding / vesicle / focal adhesion / calcium ion binding / perinuclear region of cytoplasm / enzyme binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Annexin A6 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A6 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAvila-Sakar, A.J. / Creutz, C.E. / Kretsinger, R.H.
Citation
Journal: Biochim.Biophys.Acta / Year: 1998
Title: Crystal structure of bovine annexin VI in a calcium-bound state.
Authors: Avila-Sakar, A.J. / Creutz, C.E. / Kretsinger, R.H.
#1: Journal: Biochim.Biophys.Acta / Year: 1996
Title: The Crystal Structure of Annexin Vi Indicates Relative Rotation of the Two Lobes Upon Membrane Binding
Authors: Kawasaki, H. / Avila-Sakar, A. / Creutz, C.E. / Kretsinger, R.H.
History
DepositionSep 16, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANNEXIN VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2527
Polymers76,0121
Non-polymers2406
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.404, 67.404, 200.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein ANNEXIN VI / P68 / PROTEIN III / 67-KDA-CALCIMEDIN / LIPOCORTIN VI / 67-KDA-CALELECTRIN / CHROMOBINDIN 20 / CALPHOBINDIN II


Mass: 76011.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MEMBRANE-PERIPHERAL / Organ: LIVER / References: UniProt: P79134
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.99 Å3/Da / Density % sol: 39.7 % / Description: PROBE ~1/2 THE MASS OF ANNEXIN VI
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOUR DIFFUSION (HANGING DROP), SODIUM ACETATE 1.2 M AS PRECIPITANT, POTASSIUM CACODYLATE 0.1 M, PH 6.5, CALCIUM CHLORIDE 6.2 MM ROOM TEMPERATURE, vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlprotein1drop
20.2 MNa acetate1drop
30.02 MNa-cacodylate1drop
41.04 mM1dropCaCl2
50.11 mM1dropCa2+
61.2 MNa-acetate1reservoir
70.1 MNa-cacodylate1reservoir
86.25 mM1reservoirCaCl2
90.660 mM1reservoirCa2+

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0093
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 14, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 30424 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 20.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.307 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / Num. obs: 19075 / % possible obs: 98.7 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 99.6 % / Redundancy: 3.8 % / Num. unique obs: 1912 / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 9.8

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BOVINE ANNEXIN VI: PDB ENTRY 1ANN

1ann


Resolution: 2.9→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT B=62.4 A**2, K=0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.268 -6 %RANDOM
Rwork0.205 ---
obs0.205 18978 98.7 %-
Displacement parametersBiso mean: 28.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.4 Å
Luzzati d res low-10 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 6 117 5354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.003
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.991.5
X-RAY DIFFRACTIONx_mcangle_it3.912
X-RAY DIFFRACTIONx_scbond_it4.092
X-RAY DIFFRACTIONx_scangle_it5.482.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.327 -5.9 %
Rwork0.284 1783 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOP19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 17821 / Num. reflection Rfree: 1157 / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / Rfactor obs: 0.285

+
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