[English] 日本語
Yorodumi
- PDB-3ro2: Structures of the LGN/NuMA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ro2
TitleStructures of the LGN/NuMA complex
Components
  • G-protein-signaling modulator 2
  • peptide of Nuclear mitotic apparatus protein 1
KeywordsPROTEIN BINDING / TPR repeat / protein-protein interaction / protein-binding
Function / homology
Function and homology information


anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / Mitotic Prophase / positive regulation of chromosome segregation / microtubule minus-end / cortical microtubule / microtubule bundle ...anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / Mitotic Prophase / positive regulation of chromosome segregation / microtubule minus-end / cortical microtubule / microtubule bundle / lateral cell cortex / cell cortex region / maintenance of centrosome location / mitotic spindle astral microtubule / positive regulation of intracellular transport / regulation of metaphase plate congression / mitotic spindle midzone / positive regulation of hair follicle development / astral microtubule organization / positive regulation of spindle assembly / microtubule minus-end binding / G alpha (i) signalling events / microtubule plus-end / positive regulation of BMP signaling pathway / positive regulation of keratinocyte differentiation / spindle pole centrosome / microtubule bundle formation / microtubule plus-end binding / GDP-dissociation inhibitor activity / dynein complex binding / nucleus organization / mitotic spindle pole / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / regulation of mitotic spindle organization / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / tubulin binding / phosphatidylinositol binding / mitotic spindle organization / meiotic cell cycle / spindle microtubule / mitotic spindle / nuclear matrix / spindle pole / spindle / : / disordered domain specific binding / chromosome / cell cortex / microtubule binding / protein domain specific binding / cell division / nucleotide binding / centrosome / neuronal cell body / dendrite / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / : / NuMA N-terminal hook domain / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat ...: / : / NuMA N-terminal hook domain / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Nuclear mitotic apparatus protein 1 / G-protein-signaling modulator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShang, Y. / Wei, Z.
CitationJournal: Mol.Cell / Year: 2011
Title: LGN/mInsc and LGN/NuMA complex structures suggest distinct functions in asymmetric cell division for the Par3/mInsc/LGN and G[alpha]i/LGN/NuMA pathways
Authors: Zhu, J. / Wen, W. / Zheng, Z. / Shang, Y. / Wei, Z. / Xiao, Z. / Pan, Z. / Du, Q. / Wang, W. / Zhang, M.
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: G-protein-signaling modulator 2
B: peptide of Nuclear mitotic apparatus protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0675
Polymers40,7902
Non-polymers2763
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-11 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.305, 91.305, 178.376
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein G-protein-signaling modulator 2 / Pins homolog


Mass: 37343.672 Da / Num. of mol.: 1 / Fragment: TPR domain, UNP residues 22-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpsm2, Lgn, Pins / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8VDU0
#2: Protein/peptide peptide of Nuclear mitotic apparatus protein 1 / NuMA protein / SP-H antigen


Mass: 3446.718 Da / Num. of mol.: 1 / Fragment: UNP residues 1899-1926 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14980
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02M MgCl2, 0.1M HEPES pH 7.5, 22% w/v polyacrylic acid 5100 buffer, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→36.14 Å / Num. obs: 20308 / Observed criterion σ(I): 2

-
Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→36.14 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.891 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS; ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27091 1012 5.1 %RANDOM
Rwork0.21472 ---
obs0.21753 18723 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 18 103 2779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212738
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9433702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3065351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29924.173139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27215416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7561517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022138
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.34921727
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28732694
X-RAY DIFFRACTIONr_scbond_it3.78841011
X-RAY DIFFRACTIONr_scangle_it5.56261006
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 71 -
Rwork0.229 1319 -
obs--95.21 %
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)
18.7425-2.2603-0.74656.4580.25067.3232-0.2871-0.44130.04620.59530.19960.0002-0.32230.34490.08750.2511-0.1123-0.04150.1871-0.08660.189517.185836.7117-11.557
222.2685-10.1107-8.802610.97674.25873.70070.11721.73090.3012-0.2028-0.2394-0.185-0.4655-0.44090.12221.0704-0.433-0.18560.45710.22840.5346-12.441435.7921-13.4658
38.6269-1.0201-0.85474.6738-1.52124.16330.20060.06950.6177-0.3236-0.2555-0.1712-1.122-0.02720.0550.78390.15370.03240.25930.01810.3635-25.465951.1098-12.4691
413.05540.30181.09185.3237-0.26014.2448-0.27620.86870.2886-0.5780.14280.2395-0.5834-0.27150.13341.03280.2502-0.04150.53970.0750.5074-30.160156.4972-22.9988
57.2124-3.06070.37987.12160.82714.84390.0583-0.06240.14230.1872-0.0579-0.12210.04780.3275-0.00040.0561-0.06090.02660.0975-0.03280.038411.209127.9578-19.2341
66.0409-1.99731.70054.5692-2.94426.0229-0.09930.1842-0.2831-0.0041-0.01920.00160.37310.29350.11850.1184-0.04460.07360.0771-0.04690.07191.226918.7888-18.5805
75.56190.06082.80763.121-1.523310.6066-0.16310.1439-0.07-0.12160.14170.231-0.1254-0.39680.02140.0609-0.03070.06060.0424-0.03550.1178-12.401721.0487-15.0679
84.4183-0.33633.35032.13960.67768.4769-0.0212-0.1082-0.01780.0585-0.02780.1813-0.4102-0.28240.04910.07170.0020.06240.0144-0.01710.1007-17.280328.2202-4.8987
95.4338-1.28442.16433.69050.1585.91610.08620.03770.5578-0.1167-0.13540.1239-0.8296-0.20550.04910.28850.0750.08760.0867-0.00450.2037-22.34940.0903-5.413
100.485-0.99653.61622.4141-9.71841.4701-0.2667-0.3817-0.32430.43740.22460.3079-0.92290.52330.04210.74280.16330.60021.2770.65270.858811.787327.6718-6.6209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 46
2X-RAY DIFFRACTION2B1992 - 2005
3X-RAY DIFFRACTION3A269 - 309
4X-RAY DIFFRACTION4A310 - 344
5X-RAY DIFFRACTION5A47 - 87
6X-RAY DIFFRACTION6A88 - 128
7X-RAY DIFFRACTION7A129 - 188
8X-RAY DIFFRACTION8A189 - 228
9X-RAY DIFFRACTION9A229 - 268
10X-RAY DIFFRACTION10B2006 - 2013

+
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://pdbjlvh1.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