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- PDB-2yma: X-ray structure of the Yos9 dimerization domain -

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Basic information

Entry
Database: PDB / ID: 2yma
TitleX-ray structure of the Yos9 dimerization domain
ComponentsPROTEIN OS-9 HOMOLOG
KeywordsCARBOHYDRATE BINDING PROTEIN / QUALITY CONTROL / ENDOPLASMIC RETICULUM-ASSOCIATED PROTEIN DEGRADATION / HRD COMPLEX / MISFOLDED PROTEINS / ENDOPLASMIC RETICULUM
Function / homology
Function and homology information


detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / ubiquitin-dependent glycoprotein ERAD pathway / Hrd1p ubiquitin ligase ERAD-L complex / oligosaccharide binding / retrograde protein transport, ER to cytosol / ERAD pathway / endoplasmic reticulum unfolded protein response / endoplasmic reticulum lumen ...detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / ubiquitin-dependent glycoprotein ERAD pathway / Hrd1p ubiquitin ligase ERAD-L complex / oligosaccharide binding / retrograde protein transport, ER to cytosol / ERAD pathway / endoplasmic reticulum unfolded protein response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding
Similarity search - Function
Diaminopimelate Epimerase; Chain A, domain 1 - #60 / Yos9, dimerzation domain / Protein OS-9-like / Yos9 dimerzation domain / Protein OS9-like domain / Glucosidase II beta subunit-like protein / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Diaminopimelate Epimerase; Chain A, domain 1 ...Diaminopimelate Epimerase; Chain A, domain 1 - #60 / Yos9, dimerzation domain / Protein OS-9-like / Yos9 dimerzation domain / Protein OS9-like domain / Glucosidase II beta subunit-like protein / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Diaminopimelate Epimerase; Chain A, domain 1 / Endoplasmic reticulum targeting sequence. / Roll / Alpha Beta
Similarity search - Domain/homology
Protein OS-9 homolog
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.545 Å
AuthorsHanna, J. / Schuetz, A. / Zimmermann, F. / Behlke, J. / Sommer, T. / Heinemann, U.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and Biochemical Basis of Yos9 Protein Dimerization and Possible Contribution to Self-Association of 3-Hydroxy-3-Methylglutaryl-Coenzyme a Reductase Degradation Ubiquitin-Ligase Complex.
Authors: Hanna, J. / Schutz, A. / Zimmermann, F. / Behlke, J. / Sommer, T. / Heinemann, U.
History
DepositionJun 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN OS-9 HOMOLOG
B: PROTEIN OS-9 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)36,5172
Polymers36,5172
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-7.3 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.800, 160.800, 97.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 280:283 OR RESSEQ 286:289 OR RESSEQ...
211CHAIN B AND (RESSEQ 280:283 OR RESSEQ 286:289 OR RESSEQ...

NCS oper: (Code: given
Matrix: (-0.782286, 0.018025, -0.622659), (0.0451, -0.995319, -0.085474), (-0.621285, -0.094947, 0.777811)
Vector: -13.2136, 55.1657, -2.10779)

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Components

#1: Protein PROTEIN OS-9 HOMOLOG / YOS9P


Mass: 18258.367 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN, RESIDUES 266-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PQLINKH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 T1R / References: UniProt: Q99220
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUAL GS AT THE N-TERMINUS AFTER TAG REMOVAL.

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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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growDetails: 0.55 M NAH2PO4, 0.55 M KH2PO4, 0.1 M TRIS, PH 5.05.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 19, 2010 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.54→32.8 Å / Num. obs: 15832 / % possible obs: 99.4 % / Observed criterion σ(I): 2.9 / Redundancy: 5.6 % / Biso Wilson estimate: 54.12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.2
Reflection shellResolution: 2.54→2.61 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: SEMET DERIVATIVE REFINED MODEL SOLVED BY MAD

Resolution: 2.545→32.793 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 22.15 / Stereochemistry target values: ML
Details: REFINED COORDINATES WAS VALIDATED USING MOLPROBITY. OUTPUT SCORES: BAD ROTAMERS, 9/220 (4.1%) RAMACHANDRAN OUTLIERS, 0/263 (0.0%); RAMACHANDRAN FAVORED 256/263 (97.3%).
RfactorNum. reflection% reflection
Rfree0.2204 790 5 %
Rwork0.1811 --
obs0.183 15831 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.359 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 68.18 Å2
Baniso -1Baniso -2Baniso -3
1--9.0506 Å20 Å20 Å2
2---9.0506 Å20 Å2
3---18.1012 Å2
Refinement stepCycle: LAST / Resolution: 2.545→32.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 0 50 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072119
X-RAY DIFFRACTIONf_angle_d1.1452880
X-RAY DIFFRACTIONf_dihedral_angle_d12.553739
X-RAY DIFFRACTIONf_chiral_restr0.08328
X-RAY DIFFRACTIONf_plane_restr0.004370
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A710X-RAY DIFFRACTIONPOSITIONAL
12B710X-RAY DIFFRACTIONPOSITIONAL0.138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5454-2.70480.27941280.21772430X-RAY DIFFRACTION97
2.7048-2.91350.29041300.20912508X-RAY DIFFRACTION100
2.9135-3.20650.26091310.1952499X-RAY DIFFRACTION100
3.2065-3.66990.24171330.18482511X-RAY DIFFRACTION100
3.6699-4.62170.18341320.15462521X-RAY DIFFRACTION99
4.6217-32.79560.2031360.18472572X-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)
10.0451-1.35741.86451.451-2.13322.71290.00570.36220.70390.27380.0572-0.6489-0.68470.4108-0.12410.31660.00110.07060.32480.02060.7322-16.871748.961811.3076
22.5011-2.11120.21753.72240.38291.1477-0.12940.05820.39010.06840.1688-0.16340.17860.178-0.05980.2460.0490.05980.2938-0.09040.3386-16.218636.014520.5204
31.4909-1.8757-1.02756.87020.19083.6114-0.26350.0931-0.05950.36150.17360.29650.204-0.1190.06120.22330.0441-0.04020.2293-0.02850.3357-9.77729.538517.604
41.9923-1.690.18295.673-0.73430.1963-0.1569-0.28560.03870.53520.22450.2048-0.14240.1508-0.05930.40840.10020.02410.3882-0.06190.2611-12.776519.401818.5776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 265:310)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 311:399)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 266:343)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 344:397)

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