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- PDB-4o8q: Crystal structure of bovine MHD domain of the COPI delta subunit ... -

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Basic information

Entry
Database: PDB / ID: 4o8q
TitleCrystal structure of bovine MHD domain of the COPI delta subunit at 2.15 A resolution
ComponentsCoatomer subunit delta
KeywordsPROTEIN TRANSPORT / MHD
Function / homology
Function and homology information


cerebellar Purkinje cell layer maturation / Golgi localization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI-coated vesicle / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / pigmentation / endoplasmic reticulum to Golgi vesicle-mediated transport ...cerebellar Purkinje cell layer maturation / Golgi localization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI-coated vesicle / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / pigmentation / endoplasmic reticulum to Golgi vesicle-mediated transport / adult locomotory behavior / protein transport / Golgi membrane / endoplasmic reticulum / cytosol
Similarity search - Function
Coatomer delta subunit / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Coatomer subunit delta
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.15 Å
AuthorsLahav, A. / Rozenberg, H. / Cassel, D. / Adir, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the bovine COPI delta subunit mu homology domain at 2.15 angstrom resolution.
Authors: Lahav, A. / Rozenberg, H. / Parnis, A. / Cassel, D. / Adir, N.
History
DepositionDec 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit delta
B: Coatomer subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2153
Polymers55,1682
Non-polymers461
Water4,125229
1
A: Coatomer subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6302
Polymers27,5841
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coatomer subunit delta


Theoretical massNumber of molelcules
Total (without water)27,5841
Polymers27,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.092, 110.333, 145.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coatomer subunit delta / Archain / Delta-coat protein / Delta-COP


Mass: 27584.244 Da / Num. of mol.: 2 / Fragment: MHD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARCN1, COPD / Plasmid: pKM260 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53619
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.0759.91
2
Crystal grow
Temperature (K)Crystal-IDDetailsPH range
29310.2M Sodium citrate tribasic dehydrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K7.5; 7.5
29320.4M NaCl, 0.1M Hepes 7.5, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-410.9791
SYNCHROTRONESRF ID14-420.9394
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDApr 28, 2013
ADSC QUANTUM 315r2CCDDec 7, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL, SI(111) OR SI(311)SINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL, SI(111) OR SI(311)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.93941
ReflectionResolution: 1.96→50 Å / Num. obs: 43300 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.055 / Net I/σ(I): 28.2
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.487 / % possible all: 77.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASER(phenix)phasing
PHENIX(phenix.refine: dev_1565)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: FROM INITIAL SAD EXPERIMENT

Resolution: 2.15→19.89 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 1546 4.65 %
Rwork0.182 --
obs0.184 33217 87.7 %
all-33217 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.15→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 3 229 3979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083900
X-RAY DIFFRACTIONf_angle_d1.1595300
X-RAY DIFFRACTIONf_dihedral_angle_d14.4371457
X-RAY DIFFRACTIONf_chiral_restr0.046606
X-RAY DIFFRACTIONf_plane_restr0.004700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.21930.31581200.20892480X-RAY DIFFRACTION76
2.2193-2.29860.25941270.19632561X-RAY DIFFRACTION80
2.2986-2.39040.28881360.21342667X-RAY DIFFRACTION83
2.3904-2.4990.2651290.21142684X-RAY DIFFRACTION83
2.499-2.63050.26471400.21982858X-RAY DIFFRACTION88
2.6305-2.79490.27311400.21182900X-RAY DIFFRACTION89
2.7949-3.010.25131450.21862986X-RAY DIFFRACTION91
3.01-3.31170.26361470.20533030X-RAY DIFFRACTION93
3.3117-3.7880.21011510.163113X-RAY DIFFRACTION94
3.788-4.76170.18051550.14393199X-RAY DIFFRACTION96
4.7617-19.88980.20681560.17563193X-RAY DIFFRACTION91
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)
10.3290.6109-0.40660.70170.18651.55240.088-0.1264-0.09170.3677-0.0397-0.49280.0518-0.08520.00370.26360.0248-0.04310.22670.00330.243334.85285.422488.9941
21.5466-0.16810.30511.346-0.95611.6169-0.11980.0843-0.0767-0.20610.02570.03940.1081-0.1692-0.02150.10350.0130.01220.1875-0.03770.171130.270280.236172.7632
30.36290.6205-0.40991.43331.17971.87320.1173-0.01830.0134-0.2963-0.1940.0222-0.51420.0018-0.28050.21470.0561-0.09290.1853-0.03190.202432.528792.792290.7454
41.2742-0.90880.00931.957-0.94681.37560.1385-0.0212-0.228-0.2001-0.04070.18220.0289-0.0312-0.01030.245-0.0358-0.01880.232-0.10850.25932.476994.4394112.0638
50.38690.15560.29320.327-0.38840.8099-0.01090.1947-0.0137-0.12810.05420.1485-0.1133-0.21670.10550.2984-0.06630.01590.3328-0.12710.331130.178894.7607105.77
60.36070.1488-0.65120.6008-0.23820.98460.0648-0.16870.02020.3097-0.21710.33570.2302-0.35930.03250.2824-0.03-0.01310.2222-0.03160.206429.993980.032585.3057
72.214-0.6968-1.22471.0369-0.1031.36810.16480.0608-0.148-0.0891-0.2175-0.0758-0.03670.1651-0.00210.29540.02790.00780.2820.07520.281721.626760.1631110.1341
81.5103-1.80540.48753.4521-0.12930.5748-0.1403-0.34210.13820.26520.0964-0.30730.0460.018-0.00020.2129-0.0478-0.00750.3262-0.01520.24734.279882.3742128.6651
90.6749-0.5243-0.15060.5728-0.20970.17830.1839-0.17280.1973-0.0308-0.1225-0.1349-0.01120.1547-0.00030.3726-0.04130.06160.34950.01190.451822.517468.0152111.4358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 267 through 305 )
2X-RAY DIFFRACTION2chain 'A' and (resid 306 through 351 )
3X-RAY DIFFRACTION3chain 'A' and (resid 352 through 388 )
4X-RAY DIFFRACTION4chain 'A' and (resid 389 through 441 )
5X-RAY DIFFRACTION5chain 'A' and (resid 442 through 480 )
6X-RAY DIFFRACTION6chain 'A' and (resid 481 through 511 )
7X-RAY DIFFRACTION7chain 'B' and (resid 270 through 368 )
8X-RAY DIFFRACTION8chain 'B' and (resid 369 through 471 )
9X-RAY DIFFRACTION9chain 'B' and (resid 472 through 511 )

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