[English] 日本語
Yorodumi
- PDB-4g5q: Structure of LGN GL4/Galphai1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g5q
TitleStructure of LGN GL4/Galphai1 complex
Components
  • G-protein-signaling modulator 2
  • Guanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsCELL CYCLE/SIGNALING PROTEIN / Galphai / GoLoco / Galpha signaling / asymmetric cell division / CELL CYCLE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Ran protein signal transduction / lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / G alpha (i) signalling events / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation ...Ran protein signal transduction / lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / G alpha (i) signalling events / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / G-protein alpha-subunit binding / lateral plasma membrane / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / mitotic spindle organization / Regulation of insulin secretion / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / response to peptide hormone / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / : / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / protein domain specific binding / nucleotide binding / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Tetratricopeptide repeat / Tetratricopeptide repeat ...GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Tetratricopeptide repeat / Tetratricopeptide repeat / G-protein alpha subunit, group I / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1 / G-protein-signaling modulator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
CitationJournal: To be Published
Title: Crystal Structures of the scaffolding protein LGN reveal the general mechanism by which GoLoco binding motifs inhibit the release of GDP from Galphai subunits in G-coupled heterotrimeric proteins
Authors: Jia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Guanine nucleotide-binding protein G(i) subunit alpha-1
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
C: Guanine nucleotide-binding protein G(i) subunit alpha-1
D: Guanine nucleotide-binding protein G(i) subunit alpha-1
E: G-protein-signaling modulator 2
F: G-protein-signaling modulator 2
G: G-protein-signaling modulator 2
H: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,50433
Polymers163,3308
Non-polymers4,17425
Water63135
1
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
E: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6607
Polymers40,8322
Non-polymers8275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-64 kcal/mol
Surface area16280 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
F: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0449
Polymers40,8322
Non-polymers1,2127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-59 kcal/mol
Surface area15660 Å2
MethodPISA
3
C: Guanine nucleotide-binding protein G(i) subunit alpha-1
G: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8528
Polymers40,8322
Non-polymers1,0206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-61 kcal/mol
Surface area16700 Å2
MethodPISA
4
D: Guanine nucleotide-binding protein G(i) subunit alpha-1
H: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9489
Polymers40,8322
Non-polymers1,1167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-67 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.376, 207.376, 236.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A32 - 349
221B32 - 349
112A31 - 350
222C31 - 350
113A31 - 349
223D31 - 349
114B33 - 349
224C33 - 349
115B33 - 348
225D33 - 348
116C31 - 354
226D31 - 354
117E499 - 518
227F499 - 518
118E499 - 518
228G499 - 518
119E499 - 518
229H499 - 518
1110F498 - 518
2210G498 - 518
1111F498 - 519
2211H498 - 519
1112G498 - 518
2212H498 - 518

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

-
Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha protein


Mass: 37732.918 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 25-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1, GNAI3 / Production host: Escherichia coli (E. coli) / References: UniProt: P63096
#2: Protein/peptide
G-protein-signaling modulator 2 / LGN / Pins homolog


Mass: 3099.544 Da / Num. of mol.: 4 / Fragment: GoLoco 4 (UNP RESIDUES 628-652) / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8VDU0

-
Non-polymers , 4 types, 60 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 4.5 Å3/Da / Density % sol: 72.65 % / Mosaicity: 0.173 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5M ammonium sulfate, 1.0M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, pH 5.6 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 66971 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.096 / Χ2: 1.25 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.959.70.73533011.11100
2.95-39.70.62432881.1181100
3-3.069.70.51932781.1231100
3.06-3.129.70.42632921.151100
3.12-3.199.70.36433161.1461100
3.19-3.279.70.30832871.1631100
3.27-3.359.70.25433171.21100
3.35-3.449.60.20132961.2831100
3.44-3.549.60.16933201.3341100
3.54-3.659.60.14432981.3931100
3.65-3.789.30.13333321.4391100
3.78-3.949.20.11433211.421100
3.94-4.119.50.07933181.1961100
4.11-4.339.50.07133591.2241100
4.33-4.69.50.06733551.361100
4.6-4.969.20.0733581.431100
4.96-5.4690.07133961.3461100
5.46-6.248.90.07534081.3731100
6.24-7.868.90.04934611.1661100
7.86-508.80.02336701.061199.9

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.211 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 3385 5.1 %RANDOM
Rwork0.2073 ---
obs0.209 66859 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.68 Å2 / Biso mean: 65.7073 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10914 0 249 35 11198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211346
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.97315327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57251360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86424.393535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.285152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5171565
X-RAY DIFFRACTIONr_chiral_restr0.1490.21723
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028366
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A4150.16
12B4150.16
21A4080.17
22C4080.17
31A3930.18
32D3930.18
41B4050.19
42C4050.19
51B3960.18
52D3960.18
61C4020.17
62D4020.17
71E190.16
72F190.16
81E180.16
82G180.16
91E160.26
92H160.26
101F200.21
102G200.21
111F160.25
112H160.25
121G170.28
122H170.28
LS refinement shellResolution: 2.898→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 237 -
Rwork0.317 4262 -
all-4499 -
obs--99.73 %

+
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