[English] 日本語
Yorodumi
- PDB-5f67: An exquisitely specific PDZ/target recognition revealed by the st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f67
TitleAn exquisitely specific PDZ/target recognition revealed by the structure of INAD PDZ3 in complex with TRP channel tail
Components
  • Inactivation-no-after-potential D protein
  • TRP C terminal Tail
KeywordsPROTEIN BINDING / INAD / TRP / PDZ / atypical
Function / homology
Function and homology information


phospholipase C-activating opsin-mediated signaling pathway / Ion homeostasis / TRP channels / myosin III binding / rhabdomere microvillus membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / detection of light stimulus involved in sensory perception / inaD signaling complex / cellular response to anoxia / negative regulation of opsin-mediated signaling pathway ...phospholipase C-activating opsin-mediated signaling pathway / Ion homeostasis / TRP channels / myosin III binding / rhabdomere microvillus membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / detection of light stimulus involved in sensory perception / inaD signaling complex / cellular response to anoxia / negative regulation of opsin-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / rhabdomere / store-operated calcium channel activity / detection of light stimulus involved in visual perception / cellular response to light stimulus / olfactory learning / inositol 1,4,5 trisphosphate binding / cation channel complex / retina homeostasis / inorganic cation transmembrane transport / myosin binding / phototransduction, visible light / response to light stimulus / photoreceptor activity / phototransduction / regulation of cytosolic calcium ion concentration / visual perception / mitochondrion organization / sensory perception of sound / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / sensory perception of smell / intracellular protein localization / signaling receptor complex adaptor activity / calmodulin binding / protein heterodimerization activity / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / PDZ domain / Pdz3 Domain / Ankyrin repeat / PDZ domain / PDZ domain profile. ...: / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / PDZ domain / Pdz3 Domain / Ankyrin repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein / Roll / Mainly Beta
Similarity search - Domain/homology
Transient receptor potential protein / Inactivation-no-after-potential D protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsYe, F. / Shang, Y. / Liu, W. / Zhang, M.
CitationJournal: Structure / Year: 2016
Title: An Exquisitely Specific PDZ/Target Recognition Revealed by the Structure of INAD PDZ3 in Complex with TRP Channel Tail
Authors: Ye, F. / Liu, W. / Shang, Y. / Zhang, M.
History
DepositionDec 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inactivation-no-after-potential D protein
C: TRP C terminal Tail
B: Inactivation-no-after-potential D protein
D: TRP C terminal Tail


Theoretical massNumber of molelcules
Total (without water)27,2534
Polymers27,2534
Non-polymers00
Water4,792266
1
A: Inactivation-no-after-potential D protein
C: TRP C terminal Tail


Theoretical massNumber of molelcules
Total (without water)13,6272
Polymers13,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-7 kcal/mol
Surface area6240 Å2
MethodPISA
2
B: Inactivation-no-after-potential D protein
D: TRP C terminal Tail


Theoretical massNumber of molelcules
Total (without water)13,6272
Polymers13,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-7 kcal/mol
Surface area6150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.420, 30.126, 61.454
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 351:447 )
211CHAIN B AND (RESSEQ 351:447 )
112CHAIN C AND (RESSEQ 1257:1275 )
212CHAIN D AND (RESSEQ 1257:1275 )

NCS ensembles :
ID
1
2

-
Components

#1: Protein Inactivation-no-after-potential D protein / INAD


Mass: 11676.411 Da / Num. of mol.: 2 / Fragment: PDZ 3 domain, residues 345-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD, CG3504 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24008
#2: Protein/peptide TRP C terminal Tail


Mass: 1950.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P19334*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2%(v/v) Polyethylene glycol 400, 0.1 M Imidazole pH 7.0, 24%(w/v) Polyethylene glycol monomethyl ether 5000
PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 21237 / Num. obs: 21025 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 34.9
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 9.5 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DIW

3diw


Resolution: 1.76→41.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1081 5.14 %
Rwork0.156 --
obs0.158 21022 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.05 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4711 Å20 Å2-2.0733 Å2
2--12.552 Å20 Å2
3----6.0809 Å2
Refinement stepCycle: LAST / Resolution: 1.76→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 0 266 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071747
X-RAY DIFFRACTIONf_angle_d1.1162353
X-RAY DIFFRACTIONf_dihedral_angle_d11.42627
X-RAY DIFFRACTIONf_chiral_restr0.092279
X-RAY DIFFRACTIONf_plane_restr0.005299
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A731X-RAY DIFFRACTIONPOSITIONAL
12B731X-RAY DIFFRACTIONPOSITIONAL0.041
21C130X-RAY DIFFRACTIONPOSITIONAL
22D130X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7597-1.83980.27731280.20582399X-RAY DIFFRACTION97
1.8398-1.93680.21131380.16242482X-RAY DIFFRACTION100
1.9368-2.05810.21111210.14752518X-RAY DIFFRACTION100
2.0581-2.2170.18271560.14412474X-RAY DIFFRACTION100
2.217-2.44010.17911300.14722510X-RAY DIFFRACTION100
2.4401-2.79310.20011390.16052524X-RAY DIFFRACTION100
2.7931-3.51870.14981230.15292520X-RAY DIFFRACTION99
3.5187-41.78260.18931460.15692514X-RAY DIFFRACTION95
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)
10.0161-0.01060.00510.0180.00140.0080.0391-0.11550.26530.1497-0.0639-0.0999-0.2159-0.26360.00010.1610.0295-0.00720.16770.00680.158620.00729.682935.2153
20.0847-0.02550.04670.0102-0.0320.1054-0.02-0.0134-0.03160.01820.0166-0.03650.11470.13520.0050.1114-0.01570.01780.11530.00990.100525.80791.29722.9593
30.04560.01350.03460.0849-0.01450.03350.05610.144-0.07980.07580.01440.05690.1262-0.24860.00060.1374-0.02330.01250.13640.00990.128511.4728-0.258520.8989
40.29780.15380.03650.08210.00190.16610.0506-0.084-0.2635-0.0238-0.0221-0.01440.24630.0540.06410.15230.04260.01050.0989-0.00160.183824.4074-6.193118.3749
50.04660.0116-0.02420.0460.00120.0302-0.0681-0.03740.01760.0006-0.07590.0218-0.0687-0.0965-0.00270.1204-0.01660.00540.11780.02610.129917.55934.969425.3932
60.0072-0.01360.00350.0298-0.01630.0210.0613-0.04870.0911-0.0176-0.0554-0.0679-0.1101-0.22850.00010.1506-0.0029-0.00670.1710.00380.11416.694411.301724.6736
70.02480.01180.01920.02170.06710.22550.0720.05510.1973-0.1242-0.11740.0147-0.107-0.0927-0.08290.1308-0.00020.01430.07990.02430.185117.444510.255714.962
80.1281-0.08280.02840.09880.00250.08770.061-0.0080.1612-0.0193-0.01530.05750.03420.04950.05450.0841-0.00510.01770.13820.0140.094522.97282.64224.2368
90.4479-0.30720.09240.2363-0.07850.0280.13420.0894-0.0054-0.17320.127-0.00660.0374-0.07090.05520.2514-0.04680.04610.527-0.05580.186327.4611-2.29493.2075
100.0185-0.0014-0.00910.00060.00330.0177-0.07750.0107-0.0111-0.0306-0.0575-0.03180.0339-0.0236-0.00050.22420.00380.02130.1259-0.03490.176919.7144-10.211710.8595
111.0973-0.40180.09880.147-0.0360.0091-0.05040.12170.2149-0.05380.0541-0.01460.0791-0.016-0.02830.145-0.0179-0.010.1551-0.03770.078719.7057-4.94777.6617
120.01740.0006-0.01480.0118-0.00620.01490.01360.1132-0.1593-0.0743-0.0083-0.05570.1733-0.2011-00.1688-0.0234-0.0090.1820.01310.1558-8.4235-0.1453-4.4996
130.1348-0.0159-0.07460.0287-0.00910.1045-0.0549-0.00720.0465-0.02290.0729-0.0154-0.1910.06680.01550.12380.014-0.00740.12790.00910.0992-2.79218.25877.7796
140.0884-0.0306-0.0160.0408-0.04710.12880.047-0.15850.0857-0.03480.03330.0835-0.0704-0.22310.01130.12610.0203-0.00940.12010.01560.1474-17.16049.79329.7347
150.0883-0.0079-0.02540.0354-0.00560.08-0.04850.0440.1957-0.0041-0.0028-0.041-0.23740.10130.00190.1606-0.0335-0.0150.10150.01370.1873-4.261915.749912.3583
160.06910.0284-0.03330.0250.0210.1036-0.03990.13840.0260.0353-0.0046-0.0640.0495-0.2422-0.00030.12420.0057-0.0010.13150.00930.1162-11.58930.39375.7773
170.0208-0.0165-0.02620.02520.05960.1560.009-0.0614-0.17950.0256-0.04520.01110.0483-0.0993-0.10950.1352-0.0049-0.00150.07560.02830.1667-11.2359-0.698215.7487
180.04130.04740.00170.05370.0018-0.00020.0483-0.0209-0.15620.0024-0.00540.0291-0.01630.10180.00130.09660.0033-0.01390.12350.01760.1079-5.01176.19296.936
190.1265-0.0214-0.00520.04640.00440.00230.0326-0.07610.020.04230.0229-0.0212-0.0327-0.01240.02070.29710.0402-0.06710.5459-0.06730.1806-1.317911.851827.5085
200.00880.00020.00780.00040.00250.0192-0.07730.0330.0281-0.0501-0.00670.00440.0212-0.0176-0.00030.22090.0212-0.03620.1782-0.01920.1554-9.034119.7819.8376
210.48580.32850.11180.25450.07660.026-0.1172-0.065-0.16520.16230.1634-0.07580.0469-0.05480.00830.14620.04180.03820.1782-0.04120.0952-9.061814.525523.0529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 351:360)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 361:376)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 377:396)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 397:411)
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESSEQ 412:416)
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESSEQ 417:425)
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESSEQ 426:435)
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESSEQ 436:448)
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESSEQ 1257:1261)
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESSEQ 1262:1266)
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESSEQ 1267:1275)
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESSEQ 351:360)
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESSEQ 361:376)
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESSEQ 377:396)
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESSEQ 397:411)
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESSEQ 412:425)
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESSEQ 426:435)
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESSEQ 436:447)
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESSEQ 1257:1261)
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESSEQ 1262:1266)
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESSEQ 1267:1275)

+
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