[English] 日本語
Yorodumi
- PDB-1hak: CRYSTAL STRUCTURE OF RECOMBINANT HUMAN PLACENTAL ANNEXIN V COMPLE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hak
TitleCRYSTAL STRUCTURE OF RECOMBINANT HUMAN PLACENTAL ANNEXIN V COMPLEXED WITH K-201 AS A CALCIUM CHANNEL ACTIVITY INHIBITOR
ComponentsANNEXIN VAnnexin A5
KeywordsCALCIUM/PHOSPHOLIPID-BINDING / ANNEXIN V / LIPOCORTIN V / ENDONEXIN II / PLACENTA ANTICOAGULANT PROTEIN-I / 35KDA CALELECTRIN / INHIBITOR OF BLOOD COAGULATION / CALCIUM-PHOSPHOLIPID-BINDING complex
Function / homology
Function and homology information


phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / phosphatidylserine binding / : / phospholipid binding / sarcolemma / blood coagulation / Platelet degranulation ...phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / phosphatidylserine binding / : / phospholipid binding / sarcolemma / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / external side of plasma membrane / focal adhesion / calcium ion binding / negative regulation of apoptotic process / signal transduction / extracellular exosome / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A5 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A5 / 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
Chem-K21 / Annexin A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAgo, H. / Inagaki, E. / Miyano, M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of annexin V with its ligand K-201 as a calcium channel activity inhibitor.
Authors: Kaneko, N. / Ago, H. / Matsuda, R. / Inagaki, E. / Miyano, M.
#1: Journal: Drug Dev.Res. / Year: 1994
Title: New 1,4-Bezothiazepin Derivative, K201, Demonstrates Cardioprotective Effects Against Sudden Cardiac Cell Death and Intracellular Calcium Blocking Action
Authors: Kaneko, N.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal and Molecular Structure of Human Annexin V After Refinement. Implications for Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
Authors: Huber, R. / Berendes, R. / Burger, A. / Schneider, M. / Karshikov, A. / Luecke, H. / Romisch, J. / Paques, E.
#3: Journal: J.Biochem.(Tokyo) / Year: 1987
Title: Structure and Expression of Cdna for an Inhibitor of Blood Coagulation Isolated from Human Placenta: A New Lipocortin-Like Protein
Authors: Iwasaki, A. / Suda, M. / Nakao, H. / Nagoya, T. / Saino, Y. / Arai, K. / Mizoguchi, T. / Sato, F. / Yoshizaki, H. / Hirata, M. / Miyata, T. / Shidara, Y. / Murata, M. / Maki, M.
History
DepositionDec 10, 1997Processing site: BNL
Revision 1.0Feb 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: ANNEXIN V
A: ANNEXIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8114
Polymers71,9612
Non-polymers8492
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.300, 99.300, 130.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein ANNEXIN V / Annexin A5 / LIPOCORTIN V / ENDONEXIN II / PLACENTA ANTICOAGULANT PROTEIN-I / 35KDA CALELECTRIN / INHIBITOR OF ...LIPOCORTIN V / ENDONEXIN II / PLACENTA ANTICOAGULANT PROTEIN-I / 35KDA CALELECTRIN / INHIBITOR OF BLOOD COAGULATION


Mass: 35980.707 Da / Num. of mol.: 2 / Fragment: ANNEXIN FOLD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Cellular location: CYTOPLASM / Gene: CDNA / Organ: PLACENTA / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P08758
#2: Chemical ChemComp-K21 / 4-[3-{1-(4-BENZYL)PIPERODINYL}PROPIONYL]-7-METHOXY-2,3,4,5-TERTRAHYDRO-1,4-BENZOTHIAZEPINE / K201


Mass: 424.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H32N2O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
21 mMcalcium chloride11
1ammonium sulfate11

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 14, 1995 / Details: ASYMMETRIC DOUBLE MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 104199 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.6

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AK0

1ak0


Resolution: 3→20 Å / Rfactor Rfree error: 0.0125 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE PSF FILE FOR X-PLOR REFINEMENT WAS CREATED USING QUANTA/CHARMM.
RfactorNum. reflection% reflectionSelection details
Rfree0.331 701 5 %RANDOM
Rwork0.206 ---
obs0.206 14609 97.4 %-
Displacement parametersBiso mean: 12.6 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5026 0 60 109 5195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
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_deg3.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.428
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.348 78 5 %
Rwork0.273 1626 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROAMINO.RTF
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.428
LS refinement shell
*PLUS
Rfactor obs: 0.273

+
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