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- PDB-4goe: Crystal structure of the SGTA homodimerization domain with a cova... -

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Basic information

Entry
Database: PDB / ID: 4goe
TitleCrystal structure of the SGTA homodimerization domain with a covalent modification of a single C38
ComponentsSmall glutamine-rich tetratricopeptide repeat-containing protein alpha
KeywordsPROTEIN BINDING / Four-helix bundle / Protein-protein interaction / Ubl4A ubiquitin-like domain
Function / homology
Function and homology information


TRC complex / negative regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / positive regulation of ERAD pathway / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of ubiquitin-dependent protein catabolic process / BAT3 complex binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of ubiquitin-dependent protein catabolic process / ERAD pathway ...TRC complex / negative regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / positive regulation of ERAD pathway / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of ubiquitin-dependent protein catabolic process / BAT3 complex binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of ubiquitin-dependent protein catabolic process / ERAD pathway / molecular adaptor activity / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Immunoglobulin FC, subunit C / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Small glutamine-rich tetratricopeptide repeat-containing protein alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsChartron, J.W. / VanderVelde, D.G. / Clemons Jr., W.M.
CitationJournal: Cell Rep / Year: 2012
Title: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface.
Authors: Chartron, J.W. / Vandervelde, D.G. / Clemons, W.M.
History
DepositionAug 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small glutamine-rich tetratricopeptide repeat-containing protein alpha
B: Small glutamine-rich tetratricopeptide repeat-containing protein alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5914
Polymers11,4772
Non-polymers1142
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-20 kcal/mol
Surface area5720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.726, 44.132, 63.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-102-

CL

21A-201-

HOH

31A-220-

HOH

41B-132-

HOH

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Components

#1: Protein Small glutamine-rich tetratricopeptide repeat-containing protein alpha / Alpha-SGT / Vpu-binding protein / UBP


Mass: 5738.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SGT, SGT1, SGTA / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: O43765
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% 2-propanol, 0.1 M sodium citrate, 26% PEG 400, 10 mM 2-mercaptoethanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2012
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→29.73 Å / Num. obs: 15303 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.8
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 1.8 / Num. unique all: 767 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→29.726 Å / SU ML: 0.12 / σ(F): 1.55 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1093 7.16 %RANDOM
Rwork0.1808 ---
obs0.1824 15276 98.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→29.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 0 5 107 863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006763
X-RAY DIFFRACTIONf_angle_d0.9761025
X-RAY DIFFRACTIONf_dihedral_angle_d17.166283
X-RAY DIFFRACTIONf_chiral_restr0.066120
X-RAY DIFFRACTIONf_plane_restr0.003131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.5160.25131310.23351764X-RAY DIFFRACTION99
1.516-1.59590.25071180.22841763X-RAY DIFFRACTION99
1.5959-1.69590.25251340.20021744X-RAY DIFFRACTION99
1.6959-1.82680.23791420.19731752X-RAY DIFFRACTION99
1.8268-2.01060.23281490.1751751X-RAY DIFFRACTION99
2.0106-2.30150.16671530.15181764X-RAY DIFFRACTION98
2.3015-2.89920.18961380.17761791X-RAY DIFFRACTION99
2.8992-29.73220.18711280.17341854X-RAY DIFFRACTION95

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