[English] 日本語
Yorodumi
- PDB-1kq5: C-terminal Domain of Cyclase Associated Protein with PRO 505 Repl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kq5
TitleC-terminal Domain of Cyclase Associated Protein with PRO 505 Replaced by SER (P505S)
ComponentsAdenylyl cyclase-associated protein
KeywordsSIGNALING PROTEIN / Right-handed parallel beta-helix / intertwined dimer / actin-binding
Function / homology
Function and homology information


positive regulation of actin filament depolymerization / actin cortical patch / actin filament severing / regulation of actin filament polymerization / mating projection tip / actin filament depolymerization / positive regulation of Ras protein signal transduction / positive regulation of mitochondrial fission / cAMP-mediated signaling / adenylate cyclase binding ...positive regulation of actin filament depolymerization / actin cortical patch / actin filament severing / regulation of actin filament polymerization / mating projection tip / actin filament depolymerization / positive regulation of Ras protein signal transduction / positive regulation of mitochondrial fission / cAMP-mediated signaling / adenylate cyclase binding / Neutrophil degranulation / actin filament organization / actin binding / Ras protein signal transduction / identical protein binding / cytoplasm
Similarity search - Function
Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / Adenylate cyclase associated (CAP) N terminal / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal ...Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / Adenylate cyclase associated (CAP) N terminal / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal / Pectate Lyase C-like - #70 / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Adenylyl cyclase-associated protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFedorov, A.A. / Dodatko, T. / Roswarski, D.A. / Almo, S.C.
Citation
Journal: To be Published
Title: Mutant Structures of the Actin-binding Domain of Cyclase Associated Protein (CAP) from Saccharomyces Cerevisiae
Authors: Fedorov, A.A. / Dodatko, T. / Roswarski, D.A. / Almo, S.C.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Two separate functions are encoded by the carboxyl-terminal domains of the yeast cyclase-associated protein and its mammalian homologs. Dimerization and actin binding.
Authors: Zelicof, A. / Protopopov, V. / David, D. / Lin, X.Y. / Lusgarten, V. / Gerst, J.E.
History
DepositionJan 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylyl cyclase-associated protein
B: Adenylyl cyclase-associated protein


Theoretical massNumber of molelcules
Total (without water)35,0612
Polymers35,0612
Non-polymers00
Water0
1
A: Adenylyl cyclase-associated protein


Theoretical massNumber of molelcules
Total (without water)17,5311
Polymers17,5311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylyl cyclase-associated protein


Theoretical massNumber of molelcules
Total (without water)17,5311
Polymers17,5311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Adenylyl cyclase-associated protein

B: Adenylyl cyclase-associated protein


Theoretical massNumber of molelcules
Total (without water)35,0612
Polymers35,0612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_655-x+3/2,y,-z1
Buried area2550 Å2
ΔGint-26 kcal/mol
Surface area15050 Å2
MethodPISA, PQS
4
A: Adenylyl cyclase-associated protein

A: Adenylyl cyclase-associated protein


Theoretical massNumber of molelcules
Total (without water)35,0612
Polymers35,0612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area2550 Å2
ΔGint-26 kcal/mol
Surface area15060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.37, 86.61, 160.44
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe biological assembly is a monomer generated from monomer A or from monomer B in the asymmetric unit

-
Components

#1: Protein Adenylyl cyclase-associated protein / CAP


Mass: 17530.604 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Mutation: P505S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P17555

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, lithium sulfate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 3→10 Å / Num. all: 7755 / Num. obs: 7755 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 34.6
Reflection shellResolution: 3→3.19 Å / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 12.2 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4Z

1k4z


Resolution: 3→10 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 826 10.7 %RANDOM
Rwork0.23 ---
all0.237 7755 --
obs0.237 7755 94.8 %-
Solvent computationSolvent model: flat model / Bsol: 40.8 Å2 / ksol: 0.4069 e/Å3
Displacement parametersBiso mean: 49.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 0 0 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.861.5
X-RAY DIFFRACTIONc_mcangle_it3.262
X-RAY DIFFRACTIONc_scbond_it2.512
X-RAY DIFFRACTIONc_scangle_it4.172.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 107 8.5 %
Rwork0.292 1146 -
obs-1253 93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.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