[English] 日本語
Yorodumi
- PDB-4nnm: Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (Y... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nnm
TitleTax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (YPTSII) peptide
Components
  • TIP-1 PDZ domain
  • Tax1-binding protein 3
KeywordsPROTEIN BINDING / Tax-Interacting Protein-1 / TIP-1 / PDZ / PDZ-peptide
Function / homology
Function and homology information


negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / regulation of Cdc42 protein signal transduction / negative regulation of Wnt signaling pathway / Rho protein signal transduction / beta-catenin binding / Wnt signaling pathway / fibrillar center / actin cytoskeleton / intracellular membrane-bounded organelle ...negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / regulation of Cdc42 protein signal transduction / negative regulation of Wnt signaling pathway / Rho protein signal transduction / beta-catenin binding / Wnt signaling pathway / fibrillar center / actin cytoskeleton / intracellular membrane-bounded organelle / negative regulation of cell population proliferation / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tax1-binding protein 3 / : / 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
Tax1-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionNov 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Jan 21, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tax1-binding protein 3
B: Tax1-binding protein 3
C: TIP-1 PDZ domain
D: TIP-1 PDZ domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4886
Polymers26,3044
Non-polymers1842
Water2,954164
1
A: Tax1-binding protein 3
C: TIP-1 PDZ domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2443
Polymers13,1522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-4 kcal/mol
Surface area7210 Å2
MethodPISA
2
B: Tax1-binding protein 3
D: TIP-1 PDZ domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2443
Polymers13,1522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-4 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.009, 35.043, 65.626
Angle α, β, γ (deg.)79.62, 87.61, 90.00
Int Tables number1
Space group name H-MP1
DetailsTIP-1 PDZ domain bound to peptide

-
Components

#1: Protein Tax1-binding protein 3 / Glutaminase-interacting protein 3 / Tax interaction protein 1 / TIP-1 / Tax-interacting protein 1


Mass: 12459.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAX1BP3, TIP1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / References: UniProt: O14907
#2: Protein/peptide TIP-1 PDZ domain


Mass: 692.801 Da / Num. of mol.: 2 / Source method: obtained synthetically
#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.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40% (w/v) polyethylene glycol (PEG) 3350, 0.15 M potassium thiocyanate (KSCN), 0.1 M 2-ethanesulfonic acid (MES), pH 6.0, 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: 1.6→19.308 Å / Num. all: 31186 / Num. obs: 30055 / % possible obs: 96.4 % / Observed criterion σ(F): 4.9 / Observed criterion σ(I): 17.48
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.6-1.693.5751960.395195.4
1.7-1.835.9548322.7195.4
1.84-210.14475512.5196.3
2.01-2.2316.8543817.3196.5
2.24-2.5722.9539225.2197
2.58-3.1431.5533613.6197.5

-
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: 3SFJ

3sfj


Resolution: 1.6→19.308 Å / SU ML: 0.24 / Cross valid method: omit peptide density / σ(F): 1.99 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1467 4.88 %In thin shells
Rwork0.2048 ---
obs0.2069 30050 96.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.524 Å2 / ksol: 0.455 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9851 Å20.2691 Å2-0.9302 Å2
2--3.0359 Å21.8044 Å2
3---1.9492 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 12 164 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071891
X-RAY DIFFRACTIONf_angle_d1.0672546
X-RAY DIFFRACTIONf_dihedral_angle_d15.961736
X-RAY DIFFRACTIONf_chiral_restr0.067290
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.30651360.24872787X-RAY DIFFRACTION95
1.6572-1.72350.27081440.23142816X-RAY DIFFRACTION95
1.7235-1.80190.34121430.23152895X-RAY DIFFRACTION96
1.8019-1.89680.27331530.22042807X-RAY DIFFRACTION96
1.8968-2.01550.24121470.20562870X-RAY DIFFRACTION96
2.0155-2.17090.27881490.19932836X-RAY DIFFRACTION96
2.1709-2.38910.24391410.18562873X-RAY DIFFRACTION97
2.3891-2.73390.2211540.20012907X-RAY DIFFRACTION97
2.7339-3.44130.21421530.19042897X-RAY DIFFRACTION98
3.4413-19.30910.25531470.20882895X-RAY DIFFRACTION98

+
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