[English] 日本語
Yorodumi
- PDB-1y1a: CRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1y1a
TitleCRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN
ComponentsCalcium and integrin binding 1 (calmyrin)
KeywordsMETAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN / INTEGRIN / EF-HAND / GLUTATHIONE / GLUTATHIOLATION
Function / homology
Function and homology information


calcium-dependent protein kinase inhibitor activity / thrombopoietin-mediated signaling pathway / endomitotic cell cycle / positive regulation of male germ cell proliferation / filopodium tip / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of microtubule depolymerization / protein serine/threonine kinase inhibitor activity / positive regulation of cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion ...calcium-dependent protein kinase inhibitor activity / thrombopoietin-mediated signaling pathway / endomitotic cell cycle / positive regulation of male germ cell proliferation / filopodium tip / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of microtubule depolymerization / protein serine/threonine kinase inhibitor activity / positive regulation of cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / platelet formation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of catalytic activity / regulation of cell division / spermatid development / positive regulation of protein targeting to membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of megakaryocyte differentiation / cytoplasmic microtubule organization / protein-membrane adaptor activity / positive regulation of substrate adhesion-dependent cell spreading / extrinsic apoptotic signaling pathway / cellular response to nerve growth factor stimulus / negative regulation of protein phosphorylation / cell periphery / response to ischemia / positive regulation of protein localization to plasma membrane / sarcolemma / positive regulation of protein serine/threonine kinase activity / cellular response to growth factor stimulus / ruffle membrane / small GTPase binding / double-strand break repair / negative regulation of neuron projection development / lamellipodium / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / growth cone / perikaryon / positive regulation of cell growth / angiogenesis / vesicle / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / cell adhesion / neuron projection / positive regulation of cell migration / positive regulation of protein phosphorylation / apical plasma membrane / cell division / axon / negative regulation of cell population proliferation / centrosome / neuronal cell body / apoptotic process / DNA damage response / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE / Calcium and integrin-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBlamey, C.J. / Ceccarelli, C. / Naik, U.P. / Bahnson, B.J.
CitationJournal: Protein Sci. / Year: 2005
Title: The crystal structure of calcium- and integrin-binding protein 1: Insights into redox regulated functions
Authors: Blamey, C.J. / Ceccarelli, C. / Naik, U.P. / Bahnson, B.J.
History
DepositionNov 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2012Group: Other
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 52 .. 191 B 52 .. 191 0.655 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS
Remark 999SEQUENCE GB 12654075 AAH00846 1 - 8 NOT IN ATOMS LIST A DELETION MUTANT OF CIB WHOSE SEQUENCE DOES ...SEQUENCE GB 12654075 AAH00846 1 - 8 NOT IN ATOMS LIST A DELETION MUTANT OF CIB WHOSE SEQUENCE DOES NOT INCLUDE THE FIRST EIGHT N-TERMINAL RESIDUES WAS USED FOR THE X-RAY STUDIES DESCRIBED IN THIS ENTRY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calcium and integrin binding 1 (calmyrin)
B: Calcium and integrin binding 1 (calmyrin)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5099
Polymers41,9612
Non-polymers5487
Water5,008278
1
A: Calcium and integrin binding 1 (calmyrin)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1014
Polymers20,9801
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calcium and integrin binding 1 (calmyrin)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4085
Polymers20,9801
Non-polymers4284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Calcium and integrin binding 1 (calmyrin)
B: Calcium and integrin binding 1 (calmyrin)
hetero molecules

A: Calcium and integrin binding 1 (calmyrin)
B: Calcium and integrin binding 1 (calmyrin)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,01818
Polymers83,9224
Non-polymers1,09614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area10400 Å2
ΔGint-225 kcal/mol
Surface area38960 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-105 kcal/mol
Surface area20470 Å2
MethodPISA
5
B: Calcium and integrin binding 1 (calmyrin)
hetero molecules

B: Calcium and integrin binding 1 (calmyrin)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,81610
Polymers41,9612
Non-polymers8558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area3610 Å2
ΔGint-94 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.222, 115.222, 268.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, -0.00237, -5.0E-5), (-0.00224, 0.95321, -0.3023), (0.00076, -0.3023, -0.95321)21.14937, 42.92139, 276.93698

-
Components

#1: Protein Calcium and integrin binding 1 (calmyrin) / CIB1


Mass: 20980.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q99828
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 6.2 Å3/Da / Density % sol: 80.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.12709 / Wavelength: 1.53578, 1.53466, 1.47954
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.127091
21.535781
31.534661
41.479541
ReflectionResolution: 2.3→50 Å / Num. all: 44410 / Num. obs: 44410 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2 / % possible all: 65.6

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→47.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2357501.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2207 5 %RANDOM
Rwork0.236 ---
all0.237 44316 --
obs0.236 44316 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.7122 Å2 / ksol: 0.353729 e/Å3
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å24.2 Å20 Å2
2--14.33 Å20 Å2
3----17.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 26 278 3256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it3.072
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 2.3→2.43 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 272 5.3 %
Rwork0.332 4867 -
obs-5139 65.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GSH.PARAMGSH.TOP

+
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