[English] 日本語
Yorodumi
- PDB-3v2u: Crystal structure of the yeast GAL regulon complex of the repress... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v2u
TitleCrystal structure of the yeast GAL regulon complex of the repressor, Gal80p, and the transducer, Gal3p, with galactose and ATP
Components
  • Galactose/lactose metabolism regulatory protein GAL80
  • Protein GAL3
KeywordsTRANSCRIPTION / Rossmann fold / GHMP superfamily / Transcription regulation
Function / homology
Function and homology information


regulation of transcription from RNA polymerase II promoter by galactose / galactokinase activity / kinase inhibitor activity / galactose metabolic process / maintenance of protein location / negative regulation of phosphorylation / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex ...regulation of transcription from RNA polymerase II promoter by galactose / galactokinase activity / kinase inhibitor activity / galactose metabolic process / maintenance of protein location / negative regulation of phosphorylation / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / nucleotide binding / negative regulation of transcription by RNA polymerase II / DNA binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
de novo design (two linked rop proteins) - #340 / Alpha-Beta Plaits - #3170 / Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal ...de novo design (two linked rop proteins) - #340 / Alpha-Beta Plaits - #3170 / Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / de novo design (two linked rop proteins) / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Ribosomal Protein S5; domain 2 - #10 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / NAD(P)-binding Rossmann-like Domain / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / alpha-D-galactopyranose / Galactose/lactose metabolism regulatory protein GAL80 / Protein GAL3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsLavy, T. / Kumar, P.R. / He, H. / Joshua-Tor, L.
CitationJournal: Genes Dev. / Year: 2012
Title: The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation.
Authors: Lavy, T. / Kumar, P.R. / He, H. / Joshua-Tor, L.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Refinement description
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galactose/lactose metabolism regulatory protein GAL80
B: Galactose/lactose metabolism regulatory protein GAL80
C: Protein GAL3
D: Protein GAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,22412
Polymers213,6164
Non-polymers1,6078
Water20,9511163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14160 Å2
ΔGint-52 kcal/mol
Surface area68350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.186, 83.221, 92.629
Angle α, β, γ (deg.)114.04, 92.88, 90.37
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Galactose/lactose metabolism regulatory protein GAL80


Mass: 48654.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GAL80, YML051W, YM9958.12, YM9827.01 / Production host: Escherichia coli (E. coli) / References: UniProt: P04387
#2: Protein Protein GAL3


Mass: 58153.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GAL3, YDR009W, YD8119.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P13045

-
Sugars , 1 types, 2 molecules

#5: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 1169 molecules

#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1163 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 10% PEG 3350, 0.1M di-sodium succinate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2010
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 251169 / Num. obs: 126106 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.1-2.143.90.481.5856222196.5
2.14-2.183.90.4381.6766216196.5
2.18-2.223.90.4111.7066299196.5
2.22-2.263.90.2871.6676241196.9
2.26-2.313.90.3321.7516292196.9
2.31-2.373.90.2581.6526255197
2.37-2.423.90.221.6746285197.2
2.42-2.493.90.1941.7446334197.3
2.49-2.563.90.1661.876284197.4
2.56-2.653.90.15226287197.5
2.65-2.743.90.1342.216318197.7
2.74-2.853.90.1182.5326333197.9
2.85-2.983.90.1032.9356340198
2.98-3.143.90.0923.4146326198
3.14-3.333.90.0834.0456376198.3
3.33-3.593.90.0764.756356198.4
3.59-3.953.90.0675.166355198.3
3.95-4.523.90.0615.6226363198.1
4.52-5.73.90.0575.416206196.1
5.7-5040.0414.6956418199.1

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Gal80p (1-435) 3BTS, Gal3p (259-520) 3V5R

3bts

3v5r


Resolution: 2.105→47.634 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 20.44 / Stereochemistry target values: ML / Details: TLS refinement, anisotropic for ligands only
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 1993 1.58 %Random
Rwork0.1497 ---
obs0.1505 125948 97.07 %-
all-251169 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.503 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.5389 Å23.1124 Å2-5.6846 Å2
2--5.7526 Å23.0121 Å2
3---0.4008 Å2
Refinement stepCycle: LAST / Resolution: 2.105→47.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14465 0 100 1163 15728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715161
X-RAY DIFFRACTIONf_angle_d1.00120615
X-RAY DIFFRACTIONf_dihedral_angle_d13.2175598
X-RAY DIFFRACTIONf_chiral_restr0.0692311
X-RAY DIFFRACTIONf_plane_restr0.0042646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1049-2.18010.24791830.189911890X-RAY DIFFRACTION93
2.1801-2.26740.23732010.189412346X-RAY DIFFRACTION96
2.2674-2.37060.22422050.171912304X-RAY DIFFRACTION97
2.3706-2.49550.2111930.160812468X-RAY DIFFRACTION97
2.4955-2.65190.24281980.164312421X-RAY DIFFRACTION97
2.6519-2.85660.20122060.160112455X-RAY DIFFRACTION98
2.8566-3.1440.19581900.154512515X-RAY DIFFRACTION98
3.144-3.59890.19712050.149912560X-RAY DIFFRACTION98
3.5989-4.53360.17842100.127512540X-RAY DIFFRACTION98
4.5336-47.64640.17022020.136812456X-RAY DIFFRACTION98
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)
11.6034-0.18120.03150.89590.12860.7670.0066-0.0879-0.05620.0320.0483-0.15420.09750.2144-00.16960.02050.00660.32380.02730.2618-3.19840.23288.3376
21.4491-0.19560.50631.17450.01621.3093-0.0103-0.2066-0.09070.1490.03610.0174-0.0216-0.00350.00570.1009-0.01210.06550.16030.02140.1693-28.36055.37612.7682
30.5296-0.333-0.13670.333-0.05190.5510.03780.0350.10320.0554-0.0315-0.2311-0.0930.4523-0.01290.1760.00160.05770.3651-0.02110.2712-12.19552.7309-20.1301
41.51150.19170.02060.6504-0.23180.69850.08240.0737-0.0993-0.03730.07030.19570.0996-0.2682-0.00010.2057-0.0499-0.02170.3528-0.04890.3269-69.4999-0.3364-31.6567
51.29590.05890.46160.9776-0.07910.99160.03850.1984-0.1051-0.141-0.00090.08390.0184-0.05440.00050.1156-0.00620.04020.1876-0.03470.1913-44.46684.0862-25.7827
60.42120.2621-0.10110.2062-0.06750.46130.0023-0.09790.0075-0.08290.01870.1879-0.1569-0.3464-0.00440.162-0.01330.05050.32430.01840.302-60.29033.1908-3.1962
71.55490.84950.26241.87630.07570.6366-0.03850.10410.2374-0.30580.04660.5655-0.2319-0.2036-0.0070.35680.067-0.05950.33030.04840.3513-61.43637.6707-42.398
80.73290.07080.24011.5313-0.68782.0785-0.0060.15410.0984-0.2107-0.0081-0.0124-0.1268-0.0482-0.00040.2804-0.01140.05410.26390.03430.2048-36.600643.259-40.3024
91.5647-0.57070.34291.5478-0.35090.6934-0.2924-0.11150.42170.49590.1344-0.6973-0.29140.1686-0.05550.4925-0.0259-0.22280.2882-0.08760.4705-10.194638.618917.0078
101.2899-0.3920.11082.21330.02491.366-0.2178-0.33110.19460.54570.20980.0023-0.3345-0.03350.00970.47610.11250.00650.2852-0.06690.2045-34.819944.863814.7699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 15:148 )A15 - 148
2X-RAY DIFFRACTION2( CHAIN A AND ( RESID 149:183 OR RESID 206:234 OR RESID 260:435 ) )A149 - 183
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 149:183 OR RESID 206:234 OR RESID 260:435 ) )A206 - 234
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 149:183 OR RESID 206:234 OR RESID 260:435 ) )A260 - 435
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 184:205 OR RESID 235:259 ) )A184 - 205
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 184:205 OR RESID 235:259 ) )A235 - 259
7X-RAY DIFFRACTION4( CHAIN B AND RESID 15:148 )B15 - 148
8X-RAY DIFFRACTION5( CHAIN B AND ( RESID 149:183 OR RESID 206:234 OR RESID 260:435 ) )B149 - 183
9X-RAY DIFFRACTION5( CHAIN B AND ( RESID 149:183 OR RESID 206:234 OR RESID 260:435 ) )B206 - 234
10X-RAY DIFFRACTION5( CHAIN B AND ( RESID 149:183 OR RESID 206:234 OR RESID 260:435 ) )B260 - 435
11X-RAY DIFFRACTION6( CHAIN B AND ( RESID 184:205 OR RESID 235:259 ) )B184 - 205
12X-RAY DIFFRACTION6( CHAIN B AND ( RESID 184:205 OR RESID 235:259 ) )B235 - 259
13X-RAY DIFFRACTION7( CHAIN C AND ( RESID 2:240 OR RESID 511:520 ) )C2 - 240
14X-RAY DIFFRACTION7( CHAIN C AND ( RESID 2:240 OR RESID 511:520 ) )C511 - 520
15X-RAY DIFFRACTION8( CHAIN C AND RESID 241:510 )C241 - 510
16X-RAY DIFFRACTION9( CHAIN D AND ( RESID 2:240 OR RESID 511:520 ) )D2 - 240
17X-RAY DIFFRACTION9( CHAIN D AND ( RESID 2:240 OR RESID 511:520 ) )D511 - 520
18X-RAY DIFFRACTION10( CHAIN D AND RESID 241:510 )D241 - 510

+
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