[English] 日本語
Yorodumi
- PDB-3sjb: Crystal structure of S. cerevisiae Get3 in the open state in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sjb
TitleCrystal structure of S. cerevisiae Get3 in the open state in complex with Get1 cytosolic domain
Components
  • ATPase GET3
  • Golgi to ER traffic protein 1
KeywordsHYDROLASE/TRANSPORT PROTEIN / Coiled-coil / receptor complex / TA-protein biogenesis / GET pathway / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


establishment of protein localization to endoplasmic reticulum membrane / GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion ...establishment of protein localization to endoplasmic reticulum membrane / GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / protein transmembrane transporter activity / mitophagy / protein-membrane adaptor activity / protein folding chaperone / guanyl-nucleotide exchange factor activity / mitochondrial membrane / unfolded protein binding / response to heat / cellular response to oxidative stress / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Get 1, fungi / Helix hairpin bin / Get1 family / CHD5-like protein / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Helix hairpin bin domain superfamily / Helix Hairpins ...Get 1, fungi / Helix hairpin bin / Get1 family / CHD5-like protein / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Helix hairpin bin domain superfamily / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Golgi to ER traffic protein 1 / ATPase GET3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsReitz, S. / Wild, K. / Sinning, I.
CitationJournal: Science / Year: 2011
Title: Structural basis for tail-anchored membrane protein biogenesis by the Get3-receptor complex.
Authors: Stefer, S. / Reitz, S. / Wang, F. / Wild, K. / Pang, Y.Y. / Schwarz, D. / Bomke, J. / Hein, C. / Lohr, F. / Bernhard, F. / Denic, V. / Dotsch, V. / Sinning, I.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_conn.ptnr2_label_seq_id / _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: ATPase GET3
B: ATPase GET3
C: Golgi to ER traffic protein 1
D: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9509
Polymers103,5054
Non-polymers4455
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-96 kcal/mol
Surface area34910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.900, 112.900, 310.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein ATPase GET3


Mass: 40464.730 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: GET3, ARR4, YDL100C, D2371 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q12154, Hydrolases; Acting on acid anhydrides
#2: Protein Golgi to ER traffic protein 1


Mass: 11287.648 Da / Num. of mol.: 2 / Fragment: Get1 cytosolic domain from residue 19 to 103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET1, MDM39, YGL020C / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53192
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 M LiCl, 20% PEG 6000, 0.1 M Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3.3→93.3 Å / Num. obs: 18481 / % possible obs: 99.7 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 4.9 % / Rsym value: 0.092
Reflection shellResolution: 3.3→3.48 Å / % possible all: 95.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WOJ

2woj


Resolution: 3.3→48.887 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 941 5.11 %random
Rwork0.1946 ---
obs0.197 18397 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 103.091 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1929 Å20 Å20 Å2
2---2.1929 Å2-0 Å2
3---4.3857 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5802 0 21 0 5823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095917
X-RAY DIFFRACTIONf_angle_d1.1947969
X-RAY DIFFRACTIONf_dihedral_angle_d19.3722213
X-RAY DIFFRACTIONf_chiral_restr0.075886
X-RAY DIFFRACTIONf_plane_restr0.0041029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.4740.29381550.23572399X-RAY DIFFRACTION100
3.474-3.69160.23331310.19812436X-RAY DIFFRACTION100
3.6916-3.97650.23761280.16652453X-RAY DIFFRACTION100
3.9765-4.37640.2341250.15212478X-RAY DIFFRACTION100
4.3764-5.00920.20451260.14632495X-RAY DIFFRACTION100
5.0092-6.30890.2081420.18742533X-RAY DIFFRACTION100
6.3089-48.89250.27451340.23482662X-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)
12.1432-0.6934-0.72781.1653-0.06411.1641-0.22510.0046-0.16810.0287-0.04590.16360.03570.18940.26410.296-0.020.02750.65420.14810.570530.6348-54.25059.0478
21.3570.00111.16281.32230.01521.30610.3118-0.9221-0.216-0.3881-0.10440.42720.0683-0.5793-0.1410.8631-0.0445-0.12541.5850.31991.074330.0448-62.244133.9007
31.9155-0.02331.06571.9573-0.07651.5501-0.2375-0.08270.14520.0165-0.0878-0.0802-0.0624-0.08940.30950.23610.017-0.02140.5920.04730.5235-1.1104-40.84926.7329
42.40560.29980.69911.2476-0.00851.4367-0.4849-1.35630.6812-0.23730.38650.07970.0452-0.43550.24740.89620.3692-0.25341.4147-0.44861.0895-0.0796-25.890229.7652
50.7317-0.6906-0.96271.947-0.82292.8361-0.00910.06780.0753-0.07660.50960.17110.27820.4809-0.25460.6024-0.1010.14080.84960.22790.64176.4568-58.633937.3594
6-0.27290.18450.7844-0.1953-0.09191.08220.21150.14330.49060.05580.0929-0.0595-0.02990.3186-0.38740.9748-0.1336-0.11611.1808-0.31380.903423.3108-28.263637.3276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and ((resseq 4:88) or (resseq 158:170) or (resseq 233:354))
2X-RAY DIFFRACTION2chain A and ((resseq 89:157) or (resseq 172:232))
3X-RAY DIFFRACTION3chain B and ((resseq 4:88) or (resseq 158:170) or (resseq 233:354))
4X-RAY DIFFRACTION4chain B and ((resseq 89:157) or (resseq 172:232))
5X-RAY DIFFRACTION5chain C and resseq 20:82
6X-RAY DIFFRACTION6chain D and resseq 19:90

+
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