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- PDB-4a20: Crystal structure of the Ubl domain of Mdy2 (Get5) at 1.78A -

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Basic information

Entry
Database: PDB / ID: 4a20
TitleCrystal structure of the Ubl domain of Mdy2 (Get5) at 1.78A
ComponentsUBIQUITIN-LIKE PROTEIN MDY2
KeywordsPROTEIN BINDING / GET-PATHWAY / TAIL-ANCHORED PROTEINS
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / TRC complex / tail-anchored membrane protein insertion into ER membrane / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / cytoplasmic stress granule / protein-folding chaperone binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSimon, A.C. / Simpson, P.J. / Murray, J.W. / Isaacson, R.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of the Sgt2/Get5 Complex Provides Insights Into Get-Mediated Targeting of Tail-Anchored Membrane Proteins
Authors: Simon, A.C. / Simpson, P.J. / Goldstone, R.M. / Krysztofinska, E.M. / Murray, J.W. / High, S. / Isaacson, R.L.
History
DepositionSep 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Feb 13, 2013Group: Database references
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-LIKE PROTEIN MDY2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4054
Polymers11,1171
Non-polymers2883
Water82946
1
A: UBIQUITIN-LIKE PROTEIN MDY2
hetero molecules

A: UBIQUITIN-LIKE PROTEIN MDY2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8108
Polymers22,2342
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2420 Å2
ΔGint-79.1 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.190, 47.190, 78.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein UBIQUITIN-LIKE PROTEIN MDY2 / GOLGI TO ER TRAFFIC PROTEIN 5 / MATING-DEFICIENT PROTEIN 2 / TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24


Mass: 11116.803 Da / Num. of mol.: 1 / Fragment: GET5 UBL-LIKE DOMAIN, RESIDUES 70-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12285
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.83 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 3 M AMMONIUM SULFATE, 100 MM SODIUM CITRATE PH 5.5 MIXED WITH AN EQUAL VOLUME OF PROTEIN AT 6MG/ML, HANGING DROP VAPOUR DIFFUSION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→40.87 Å / Num. obs: 10128 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.72 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.75
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M62

3m62


Resolution: 1.78→19.77 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.391 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24825 486 4.8 %RANDOM
Rwork0.20113 ---
obs0.20327 9603 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.78→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms622 0 15 46 683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022651
X-RAY DIFFRACTIONr_bond_other_d0.0010.02423
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.997885
X-RAY DIFFRACTIONr_angle_other_deg0.96831063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85126.52223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31515124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02101
X-RAY DIFFRACTIONr_nbd_refined0.2210.298
X-RAY DIFFRACTIONr_nbd_other0.1840.2407
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2300
X-RAY DIFFRACTIONr_nbtor_other0.0950.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1550.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.720.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2491.5405
X-RAY DIFFRACTIONr_mcbond_other0.3831.5157
X-RAY DIFFRACTIONr_mcangle_it2.0542665
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5763246
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3584.5219
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 37 -
Rwork0.312 692 -
obs--99.86 %
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)
115.30215.3314-6.98634.904-4.557710.4615-0.0039-0.0267-0.0834-0.15820.0712-0.32670.2810.1518-0.06720.10110.06630.05840.1065-0.01720.191241.8991-1.4217-0.04
28.12112.104-1.66974.0024-1.56652.09860.0841-0.141-0.2845-0.3868-0.0466-0.04970.1005-0.4135-0.03750.1127-0.0383-0.00360.18510.03090.128728.0273-6.67625.3369
34.00140.754-0.86363.1453-0.76593.705-0.21050.34510.1798-0.55270.18830.02730.3119-0.57810.02230.1564-0.01060.01210.1570.03450.088429.87112.3641-2.9944
43.05471.3277-0.9755.3782-1.85020.7450.0897-0.1723-0.00860.2307-0.209-0.4083-0.11830.06030.11930.13920.06910.00410.16820.03710.190436.15868.98275.4304
515.7371-0.43541.45011.09811.37832.60770.0634-0.36570.2444-0.08420.017-0.0117-0.1218-0.1368-0.08050.06970.00650.02010.10480.03680.10832.41540.34446.9271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A70 - 77
2X-RAY DIFFRACTION2A78 - 89
3X-RAY DIFFRACTION3A90 - 119
4X-RAY DIFFRACTION4A120 - 136
5X-RAY DIFFRACTION5A137 - 151

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