[English] 日本語
Yorodumi
- PDB-9imp: The complex of PDZ3 and PBM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9imp
TitleThe complex of PDZ3 and PBM
Components
  • INSC spindle orientation adaptor protein
  • Partitioning defective 3 homolog
KeywordsPEPTIDE BINDING PROTEIN / Complex / protein
Function / homology
Function and homology information


Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / PAR polarity complex / apical constriction / asymmetric cell division / establishment of centrosome localization / establishment of epithelial cell polarity ...Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / PAR polarity complex / apical constriction / asymmetric cell division / establishment of centrosome localization / establishment of epithelial cell polarity / positive regulation of myelination / lateral loop / bicellular tight junction assembly / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of peptidyl-threonine phosphorylation / myelination in peripheral nervous system / phosphatidylinositol-3-phosphate binding / protein targeting to membrane / wound healing, spreading of cells / centrosome localization / apical junction complex / establishment of cell polarity / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / bicellular tight junction / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / endomembrane system / phosphatidylinositol binding / adherens junction / microtubule cytoskeleton organization / spindle / cell junction / intracellular protein localization / cell-cell junction / cell cortex / protein phosphatase binding / cell adhesion / apical plasma membrane / cell division / neuronal cell body / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Protein inscuteable homologue, LGN-binding domain / Protein inscuteable homologue, LGN-binding domain superfamily / Inscuteable LGN-binding domain / Inscuteable / Protein inscuteable homologue, C-terminal domain / Protein inscuteable C-terminal / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / : / Armadillo/beta-catenin-like repeats ...Protein inscuteable homologue, LGN-binding domain / Protein inscuteable homologue, LGN-binding domain superfamily / Inscuteable LGN-binding domain / Inscuteable / Protein inscuteable homologue, C-terminal domain / Protein inscuteable C-terminal / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / : / Armadillo/beta-catenin-like repeats / Armadillo / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
INSC spindle orientation adaptor protein / Partitioning defective 3 homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsHuang, S.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31871394 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: mInsc coordinates Par3 and NuMA condensates for assembly of the spindle orientation machinery in asymmetric cell division.
Authors: Huang, S. / Fu, M. / Gu, A. / Zhao, R. / Liu, Z. / Hua, W. / Mao, Y. / Wen, W.
History
DepositionJul 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Partitioning defective 3 homolog
G: INSC spindle orientation adaptor protein
B: Partitioning defective 3 homolog
H: INSC spindle orientation adaptor protein
C: Partitioning defective 3 homolog
I: INSC spindle orientation adaptor protein
D: Partitioning defective 3 homolog
J: INSC spindle orientation adaptor protein
E: Partitioning defective 3 homolog
K: INSC spindle orientation adaptor protein
F: Partitioning defective 3 homolog
L: INSC spindle orientation adaptor protein


Theoretical massNumber of molelcules
Total (without water)78,52612
Polymers78,52612
Non-polymers00
Water73941
1
A: Partitioning defective 3 homolog
G: INSC spindle orientation adaptor protein
D: Partitioning defective 3 homolog
J: INSC spindle orientation adaptor protein
E: Partitioning defective 3 homolog
K: INSC spindle orientation adaptor protein

B: Partitioning defective 3 homolog
H: INSC spindle orientation adaptor protein
C: Partitioning defective 3 homolog
I: INSC spindle orientation adaptor protein
F: Partitioning defective 3 homolog
L: INSC spindle orientation adaptor protein


Theoretical massNumber of molelcules
Total (without water)78,52612
Polymers78,52612
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area12760 Å2
ΔGint-70 kcal/mol
Surface area28810 Å2
MethodPISA
2
A: Partitioning defective 3 homolog
G: INSC spindle orientation adaptor protein
D: Partitioning defective 3 homolog
J: INSC spindle orientation adaptor protein
E: Partitioning defective 3 homolog
K: INSC spindle orientation adaptor protein

B: Partitioning defective 3 homolog
H: INSC spindle orientation adaptor protein
C: Partitioning defective 3 homolog
I: INSC spindle orientation adaptor protein
F: Partitioning defective 3 homolog
L: INSC spindle orientation adaptor protein


Theoretical massNumber of molelcules
Total (without water)78,52612
Polymers78,52612
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area12320 Å2
ΔGint-64 kcal/mol
Surface area29250 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-58 kcal/mol
Surface area28130 Å2
MethodPISA
4
A: Partitioning defective 3 homolog
G: INSC spindle orientation adaptor protein
D: Partitioning defective 3 homolog
J: INSC spindle orientation adaptor protein
E: Partitioning defective 3 homolog
K: INSC spindle orientation adaptor protein


Theoretical massNumber of molelcules
Total (without water)39,2636
Polymers39,2636
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-35 kcal/mol
Surface area15010 Å2
MethodPISA
5
B: Partitioning defective 3 homolog
H: INSC spindle orientation adaptor protein
C: Partitioning defective 3 homolog
I: INSC spindle orientation adaptor protein
F: Partitioning defective 3 homolog
L: INSC spindle orientation adaptor protein


Theoretical massNumber of molelcules
Total (without water)39,2636
Polymers39,2636
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-29 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.390, 90.380, 170.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Partitioning defective 3 homolog / PAR-3 / PARD-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Atypical PKC-specific- ...PAR-3 / PARD-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Atypical PKC-specific-binding protein / ASBP


Mass: 11929.435 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pard3, Par3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z340
#2: Protein/peptide
INSC spindle orientation adaptor protein


Mass: 1158.302 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Insc / Production host: Escherichia coli (E. coli) / References: UniProt: D3Z267
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.8 M ammonium sulfate, 0.1 M citrate (pH 4.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.87→62.09 Å / Num. obs: 20641 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.3
Reflection shellResolution: 2.87→2.94 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 20641 / CC1/2: 0.847 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JUE

6jue


Resolution: 2.87→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU B: 34.733 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R: 0.974 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2823 1113 5.1 %RANDOM
Rwork0.22528 ---
obs0.22811 20641 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.214 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å2-0 Å20 Å2
2---5.36 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4564 0 0 41 4605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164661
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.6266117
X-RAY DIFFRACTIONr_angle_other_deg0.4881.57510657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9095582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.385548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.81310881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021058
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2325.5412409
X-RAY DIFFRACTIONr_mcbond_other5.2325.5412409
X-RAY DIFFRACTIONr_mcangle_it8.5049.8752964
X-RAY DIFFRACTIONr_mcangle_other8.5039.8762965
X-RAY DIFFRACTIONr_scbond_it5.3596.0312188
X-RAY DIFFRACTIONr_scbond_other5.3576.0312189
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.68410.8553154
X-RAY DIFFRACTIONr_long_range_B_refined12.3853.164653
X-RAY DIFFRACTIONr_long_range_B_other12.37853.164653
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.87→2.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 74 -
Rwork0.327 1498 -
obs--99.87 %
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)
11.61060.2244-0.43961.18050.04771.3268-0.251-0.3958-0.252-0.2296-0.1152-0.4896-0.0126-0.03580.36610.07930.06240.06560.53630.15480.582324.1615.81337.176
28.23611.34284.32221.0361-0.48434.26060.2701-0.90630.0732-0.1738-0.4089-0.23240.2348-0.24480.13880.44520.18380.10630.30820.16590.5228.936.60340.431
30.2455-0.0311-0.69235.8002-0.11512.0626-0.141-0.042-0.0042-0.2760.11010.19580.2690.03250.03090.3891-0.03240.08960.33920.00030.35510.2530.0834.161
47.04482.75180.01478.29977.60217.9878-0.4717-0.35410.0549-0.5537-0.10360.5643-0.40540.04420.57530.5003-0.03220.04970.2350.10970.3165-1.151-6.38843.047
50.102-0.1305-0.2712.05981.14732.107-0.03280.06640.13450.1421-0.2230.50620.21720.08320.25580.17310.04160.02480.4226-0.00030.5958-4.68923.58531.964
60.05290.36210.66078.1051-5.574926.8789-0.0035-0.06860.0274-0.19-0.64-0.0005-0.0891-0.65450.64350.23270.10180.01320.3666-0.0050.4774-9.24333.55933.047
71.54331.1947-0.82011.53190.48443.0416-0.34620.13390.059-0.31960.1319-0.07260.127-0.02070.21430.2944-0.09010.12950.41420.06650.493522.33228.24416.505
83.6195-2.81824.41022.2777-3.62165.79780.1232-0.1889-0.05390.12330.04210.0927-0.33230.0233-0.16530.6493-0.15060.19870.44370.00230.17625.3734.7726.215
90.41271.3333-0.11975.2531-0.74351.41520.0405-0.17710.1449-0.0881-0.0019-0.03270.0590.0815-0.03860.0401-0.12840.10750.5567-0.22350.64423.64339.82638.948
101.0621-0.2515-2.17550.10050.64455.15510.3466-0.0350.2695-0.00440.101-0.0622-0.23980.1204-0.44760.524-0.05730.00950.4255-0.02870.377328.06546.99545.404
111.31090.09181.38152.2788-2.38225.0195-0.1379-0.16280.4208-0.4789-0.5056-0.05790.6668-0.28290.64350.3511-0.0746-0.09220.6275-0.12620.2562-5.0319.72211.52
1218.00334.774917.18041.30044.516216.4586-0.115-1.18520.6809-0.0966-0.450.23220.057-1.00830.5650.71870.0739-0.13410.6804-0.19970.1933-9.7436.4141.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A580 - 685
2X-RAY DIFFRACTION2G526 - 532
3X-RAY DIFFRACTION3B580 - 685
4X-RAY DIFFRACTION4H527 - 532
5X-RAY DIFFRACTION5C580 - 685
6X-RAY DIFFRACTION6I528 - 532
7X-RAY DIFFRACTION7D580 - 685
8X-RAY DIFFRACTION8J526 - 532
9X-RAY DIFFRACTION9E581 - 685
10X-RAY DIFFRACTION10K526 - 532
11X-RAY DIFFRACTION11F581 - 685
12X-RAY DIFFRACTION12L529 - 532

+
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