[English] 日本語
Yorodumi
- PDB-6ov7: CFTR Associated Ligand (CAL) PDZ domain bound to peptide kCAL01 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ov7
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide kCAL01
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • kCAL01 peptide
KeywordsPEPTIDE BINDING PROTEIN / PDZ domain / inhibitor / complex
Function / homology
Function and homology information


negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport ...negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / transmembrane transporter binding / postsynaptic density / lysosomal membrane / Golgi membrane / dendrite / Golgi apparatus / protein-containing complex / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Golgi-associated PDZ and coiled-coil motif-containing protein / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsGill, N.P. / Madden, D.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK101451 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
CitationJournal: J.Phys.Chem.B / Year: 2019
Title: Computational Analysis of Energy Landscapes Reveals Dynamic Features That Contribute to Binding of Inhibitors to CFTR-Associated Ligand.
Authors: Holt, G.T. / Jou, J.D. / Gill, N.P. / Lowegard, A.U. / Martin, J.W. / Madden, D.R. / Donald, B.R.
History
DepositionMay 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Golgi-associated PDZ and coiled-coil motif-containing protein
B: Golgi-associated PDZ and coiled-coil motif-containing protein
C: kCAL01 peptide
D: kCAL01 peptide


Theoretical massNumber of molelcules
Total (without water)21,1444
Polymers21,1444
Non-polymers00
Water3,153175
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: kCAL01 peptide


Theoretical massNumber of molelcules
Total (without water)10,5722
Polymers10,5722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area5460 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: kCAL01 peptide


Theoretical massNumber of molelcules
Total (without water)10,5722
Polymers10,5722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-5 kcal/mol
Surface area5410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.622, 60.767, 81.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Golgi-associated PDZ and coiled-coil motif-containing protein / CFTR-associated ligand / Fused in glioblastoma / PDZ protein interacting specifically with TC10 / PIST


Mass: 9353.722 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9HD26
#2: Protein/peptide kCAL01 peptide


Mass: 1218.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Engineered / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 6 mg/mL CAL PDZ, 1 mM kCAL01 peptide, 25% (w/v) PEG 8000, 5% PEG 400, 150 mM NaCl, and 100 mM Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2016
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 27416 / % possible obs: 99.6 % / Redundancy: 6.46 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obs% possible allRmerge(I) obsCC1/2Rrim(I) all
8-9.995.3749.99132100
6-7.995.943.0335299.4
5-5.996.3444.4427100
4.85-4.996.7950.8294100
3.44-4.845.840.62193898.9
2.81-3.436.4326.94249299.8
2.44-2.86.6916.222844100
2.18-2.436.410.57328999.8
1.99-2.176.717.19362199.9
1.84-1.986.373.79394199.6
1.71-1.836.652.04424199.80.9590.7861.041

-
Processing

Software
NameVersionClassification
PHENIXversion 1.14-3260-000refinement
XDSVersion November 1, 2016data reduction
XSCALEVersion November 1, 2016data scaling
PHENIXPhaser-MR Version 1.14-3260-000phasing
PHENIXphenix.refine Version 1.14-3260-000model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+34 / Resolution: 1.71→38.42 Å / Cross valid method: THROUGHOUT
Details: ALPHA HELIX-1 OF CHAIN B APPEARS DISTORTED DUE TO DISULFIDE FORMATION. CHAIN A RETAINS NORMAL ALPHA HELICAL STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1160 4.9 %Random selection
Rwork0.182 ---
obs-23681 99.2 %-
Displacement parametersBiso mean: 23.56 Å2
Refinement stepCycle: LAST / Resolution: 1.71→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 0 175 1645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7134-1.79140.306700.28132681X-RAY DIFFRACTION96
1.7914-1.88580.268600.23642769X-RAY DIFFRACTION100
1.8858-2.0040.257700.20242814X-RAY DIFFRACTION100
2.004-2.15870.198700.17362766X-RAY DIFFRACTION100
2.1587-2.37590.214100.17532823X-RAY DIFFRACTION100
2.3759-2.71960.205600.17422817X-RAY DIFFRACTION100
2.7196-3.42610.187200.17212890X-RAY DIFFRACTION100
3.4261-38.4240.204900.16832961X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.4682 Å / Origin y: 27.6297 Å / Origin z: 30.5801 Å
111213212223313233
T0.0457 Å2-0.0014 Å20.0021 Å2-0.0449 Å20.0085 Å2--0.0428 Å2
L0.1922 °2-0.1687 °20.1997 °2-0.1574 °2-0.2453 °2--0.3094 °2
S-0.0109 Å °0.034 Å °-0.0143 Å °0.0161 Å °0.0198 Å °-0.006 Å °-0.022 Å °-0.0072 Å °-0 Å °
Refinement TLS groupSelection details: all

+
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