[English] 日本語
Yorodumi
- PDB-4q6s: CFTR Associated Ligand (CAL) PDZ bound to biotinylated peptide BT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q6s
TitleCFTR Associated Ligand (CAL) PDZ bound to biotinylated peptide BT-L-iCAL36
Components
  • BT-L-iCAL36 peptide
  • Golgi-associated PDZ and coiled-coil motif-containing protein
KeywordsTRANSPORT PROTEIN / PDZ-peptide 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 / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / Golgi-associated vesicle membrane / apical protein localization / RHOQ GTPase cycle / molecular sequestering activity / 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 / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / Golgi-associated vesicle membrane / apical protein localization / RHOQ GTPase cycle / molecular sequestering activity / 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
Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: J.Mol.Biol. / Year: 2026
Title: Sequence Engineering at Non-motif Modulator Residues Yields a Peptide That Effectively Targets a Single PDZ Protein in a Disease-relevant Cellular Context.
Authors: Amacher, J.F. / Cushing, P.R. / Vouilleme, L. / Cullati, S.N. / Deng, B. / Gerber, S.A. / Boisguerin, P. / Madden, D.R.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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_atom_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
Revision 1.3Jan 21, 2026Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
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: BT-L-iCAL36 peptide
D: BT-L-iCAL36 peptide


Theoretical massNumber of molelcules
Total (without water)22,8024
Polymers22,8024
Non-polymers00
Water4,360242
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: BT-L-iCAL36 peptide


Theoretical massNumber of molelcules
Total (without water)11,4012
Polymers11,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-4 kcal/mol
Surface area6050 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: BT-L-iCAL36 peptide


Theoretical massNumber of molelcules
Total (without water)11,4012
Polymers11,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-6 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.599, 48.167, 101.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCAL PDZ domain bound to peptide, BT-L-iCAL36

-
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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q9HD26
#2: Protein/peptide BT-L-iCAL36 peptide


Mass: 2047.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.95
Details: 16% (w/v) polyethylene glycol (PEG), 0.15 M sodium chloride, 0.01 M Tris HCl pH 7.95, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9181 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 26, 2010
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 1.45→19.732 Å / Num. all: 32531 / Num. obs: 32353 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 8.27 / Redundancy: 13.9 % / Rmerge(I) obs: 0.055 / Rsym value: 0.074 / Net I/σ(I): 24.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.41-2.9313.50.02341.7332080.054100
2.09-2.413.80.02936.9237950.066100
1.87-2.0814.20.04527.5242770.092100
1.71-1.8614.40.07918.2946230.15399.9
1.58-1.714.50.1212.9752180.23899.7
1.45-1.5714.10.2068.2772060.39599.3

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4E34 without peptide

4e34


Resolution: 1.45→19.732 Å / SU ML: 0.17 / Cross valid method: Omit map / σ(F): 2 / σ(I): 8.27 / Phase error: 17.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1615 4.99 %In thin shells
Rwork0.177 ---
obs0.1779 32353 99.5 %-
all-32531 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.439 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2854 Å2-0 Å2-0 Å2
2---0.6816 Å2-0 Å2
3----1.6038 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 0 242 1845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081674
X-RAY DIFFRACTIONf_angle_d1.4972264
X-RAY DIFFRACTIONf_dihedral_angle_d19.707663
X-RAY DIFFRACTIONf_chiral_restr0.109258
X-RAY DIFFRACTIONf_plane_restr0.008292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50180.25721610.2142992X-RAY DIFFRACTION99
1.5018-1.56190.20761620.18173032X-RAY DIFFRACTION99
1.5619-1.6330.21171610.1813032X-RAY DIFFRACTION100
1.633-1.7190.23161600.17543048X-RAY DIFFRACTION100
1.719-1.82660.17661610.17323040X-RAY DIFFRACTION100
1.8266-1.96760.20051620.16413061X-RAY DIFFRACTION100
1.9676-2.16530.18041620.16953090X-RAY DIFFRACTION100
2.1653-2.47820.20491620.17313087X-RAY DIFFRACTION100
2.4782-3.12020.18261620.18333142X-RAY DIFFRACTION100
3.1202-19.73390.18461620.17683214X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2833-0.14990.20640.5662-0.18510.58320.0079-0.0383-0.0177-0.01970.01420.04230.05880.0064-0.01790.04450.0007-0.00050.0501-0.00370.04842.701621.766640.9308
20.1288-0.18780.12111.66670.44560.39170.02140.1074-0.00390.0684-0.0268-0.25570.06930.0689-0.04430.07610.01-0.0020.118-0.01160.146217.122317.611845.9583
30.47260.39560.09780.3782-0.09610.78030.0367-0.02460.0260.0561-0.0381-0.0026-0.04380.07140.00550.0667-0.0156-0.00110.05540.00450.06046.289119.598116.809
41.15650.634-0.62490.6019-0.15640.47350.0644-0.2551-0.27170.0576-0.088-0.21740.04920.2835-0.06030.1002-0.01620.00380.1582-0.02750.165221.952224.560217.0502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A and resid 284:370
2X-RAY DIFFRACTION2Chain C and resid 0:15
3X-RAY DIFFRACTION3Chain B and resid 284:370
4X-RAY DIFFRACTION4Chain D and resid 0:15

+
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