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- PDB-3lku: Crystal structure of S. cerevisiae Get4 in complex with an N-term... -

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Basic information

Entry
Database: PDB / ID: 3lku
TitleCrystal structure of S. cerevisiae Get4 in complex with an N-terminal fragment of Get5
Components
  • UPF0363 protein YOR164C
  • Ubiquitin-like protein MDY2
KeywordsPROTEIN BINDING / ALPHA HELICAL REPEAT / TPR-LIKE
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / TRC complex / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / vesicle-mediated transport / cytoplasmic stress granule / protein-macromolecule adaptor activity / nucleus / cytosol / cytoplasm
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 / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / Single helix bin / Tetratricopeptide repeat domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...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 / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / Single helix bin / Tetratricopeptide repeat domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROLINE / Golgi to ER traffic protein 4 / Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsChartron, J.W. / Clemons Jr., W.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural characterization of the Get4/Get5 complex and its interaction with Get3.
Authors: Chartron, J.W. / Suloway, C.J. / Zaslaver, M. / Clemons, W.M.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: UPF0363 protein YOR164C
B: Ubiquitin-like protein MDY2
C: UPF0363 protein YOR164C
D: Ubiquitin-like protein MDY2
E: UPF0363 protein YOR164C
F: Ubiquitin-like protein MDY2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7778
Polymers121,5466
Non-polymers2302
Water1,51384
1
A: UPF0363 protein YOR164C
B: Ubiquitin-like protein MDY2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6313
Polymers40,5152
Non-polymers1151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-30 kcal/mol
Surface area16720 Å2
MethodPISA
2
C: UPF0363 protein YOR164C
D: Ubiquitin-like protein MDY2


Theoretical massNumber of molelcules
Total (without water)40,5152
Polymers40,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-31 kcal/mol
Surface area16850 Å2
MethodPISA
3
E: UPF0363 protein YOR164C
F: Ubiquitin-like protein MDY2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6313
Polymers40,5152
Non-polymers1151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-30 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.733, 108.733, 169.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein UPF0363 protein YOR164C


Mass: 34428.395 Da / Num. of mol.: 3 / Fragment: UNP residues 11-300
Source method: isolated from a genetically manipulated source
Details: Coexpressed with YOL111C. After affinity purification, limited proteolysis was performed with chymotrypsin. The major fragments were separated by anion exchange chromatography followed by crystallization.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: O3580, YOR164C, YOR164C/Get4 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12125
#2: Protein Ubiquitin-like protein MDY2 / Mating-deficient protein 2 / Translation machinery-associated protein 24


Mass: 6087.066 Da / Num. of mol.: 3 / Fragment: UNP residues 3-56
Source method: isolated from a genetically manipulated source
Details: Coexpressed with YOR164C. After affinity purification, limited proteolysis was performed with chymotrypsin. The major fragments were separated by anion exchange chromatography followed by crystallization.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MDY2, TMA24, YOL111C, YOL111C/Get5 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12285
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 6000, 0.1M Bis-Tris, 0.14M Ammonium sulfate, 0.01M L-proline, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97862 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2010
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.8→29.44 Å / Num. all: 29224 / Num. obs: 29191 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 20.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4190 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.6.0050refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→28.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 29.123 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Used direct SAD refinement target using selenomethioine
RfactorNum. reflection% reflectionSelection details
Rfree0.22571 1464 5 %RANDOM
Rwork0.18221 ---
all0.18436 29224 --
obs0.18436 29186 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20.99 Å20 Å2
2--1.98 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8439 0 16 84 8539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228653
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.96411694
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37351017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80524.599424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.847151536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.421528
X-RAY DIFFRACTIONr_chiral_restr0.1110.21272
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216520
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 105 -
Rwork0.252 2006 -
obs-2111 99.95 %
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)
11.10.142-1.14210.62-0.65315.50870.07630.14160.0592-0.13310.02160.0921-0.0722-0.2973-0.09790.04770.0162-0.01630.0282-0.01120.1308-8.611614.069977.0699
20.9158-0.09360.48441.5838-0.43454.8156-0.13670.148-0.0098-0.23940.235-0.06410.18980.0843-0.09830.0713-0.0614-0.00630.06790.00490.1236-10.739149.214885.9925
31.16420.0541-0.52051.34040.63926.4231-0.02890.272-0.0302-0.05710.2322-0.0246-0.18260.3534-0.20330.0314-0.051-0.0320.1518-0.00930.2183-38.89335.54167.6176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 299
2X-RAY DIFFRACTION1B3 - 54
3X-RAY DIFFRACTION1A1
4X-RAY DIFFRACTION2C9 - 297
5X-RAY DIFFRACTION2D4 - 54
6X-RAY DIFFRACTION3E9 - 299
7X-RAY DIFFRACTION3F3 - 56
8X-RAY DIFFRACTION3E1

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