[English] 日本語
Yorodumi
- PDB-4nmv: CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nmv
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(BRB-K-1) (ANSRWPTS[4-bromobenzoic-acyl-K]I)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36(BRB-K-1) peptide
Keywordsprotein transport/inhibitor / CAL / GOPC / PIST / FIG / CFTR / PDZ / PDZ-peptide / protein transport-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 / trans-Golgi network transport vesicle / apical protein localization / molecular sequestering activity / 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 / trans-Golgi network transport vesicle / apical protein localization / molecular sequestering activity / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / transmembrane transporter binding / postsynaptic density / Golgi membrane / lysosomal membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Golgi-associated PDZ and coiled-coil motif-containing protein / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
iCAL36(BRB-K-1) peptide / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: Plos One / Year: 2014
Title: Chemically Modified Peptide Scaffolds Target the CFTR-Associated Ligand PDZ Domain.
Authors: Amacher, J.F. / Zhao, R. / Spaller, M.R. / Madden, D.R.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

-
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: iCAL36(BRB-K-1) peptide
D: iCAL36(BRB-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5786
Polymers21,3944
Non-polymers1842
Water3,657203
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(BRB-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7893
Polymers10,6972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-7 kcal/mol
Surface area5260 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL36(BRB-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7893
Polymers10,6972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area5320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.986, 47.944, 97.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCAL PDZ domain bound to decameric peptide

-
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 / Fragment: UNP RESIDUES 284-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9HD26
#2: Protein/peptide iCAL36(BRB-K-1) peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 1343.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: iCAL36(BRB-K-1) peptide
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 31% (w/v) polyethylene glycol (PEG), 0.1 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.4→19.5 Å / Num. all: 34036 / Num. obs: 33913 / % possible obs: 99.6 % / Observed criterion σ(F): 7.8 / Observed criterion σ(I): 25.63
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.4-1.464.2945400.686199.1
1.47-1.586.5860740.437199.4
1.59-1.7310.8254570.256199.6
1.74-1.9418.93508214199.9
1.95-2.2334.3643027.31100
2.24-2.7345.4637935.11100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E34

4e34


Resolution: 1.4→19.5 Å / SU ML: 0.19 / Cross valid method: omit peptide density / σ(F): 2 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 1720 5.07 %In thin shells
Rwork0.1823 ---
obs0.1833 33913 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.489 Å2 / ksol: 0.428 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3457 Å20 Å20 Å2
2---0.6878 Å20 Å2
3----0.6578 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 12 203 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081533
X-RAY DIFFRACTIONf_angle_d1.1392073
X-RAY DIFFRACTIONf_dihedral_angle_d15.843574
X-RAY DIFFRACTIONf_chiral_restr0.071234
X-RAY DIFFRACTIONf_plane_restr0.006268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.44120.28551720.24422590X-RAY DIFFRACTION99
1.4412-1.48770.242860.21862692X-RAY DIFFRACTION99
1.4877-1.54090.21721720.19652584X-RAY DIFFRACTION99
1.5409-1.60250.1991720.1882605X-RAY DIFFRACTION99
1.6025-1.67540.2032860.17482685X-RAY DIFFRACTION100
1.6754-1.76370.20511720.17842658X-RAY DIFFRACTION100
1.7637-1.87410.20621450.16932668X-RAY DIFFRACTION100
1.8741-2.01870.19841130.16422699X-RAY DIFFRACTION100
2.0187-2.22160.17971720.17532662X-RAY DIFFRACTION100
2.2216-2.54250.1961390.18462718X-RAY DIFFRACTION100
2.5425-3.2010.19361190.17872780X-RAY DIFFRACTION100
3.201-19.54720.19871720.1822852X-RAY DIFFRACTION100

+
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