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- PDB-5mc7: Crystal structure of Truncated Human Coatomer Protein Complex, su... -

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Basic information

Entry
Database: PDB / ID: 5mc7
TitleCrystal structure of Truncated Human Coatomer Protein Complex, subunit Z1 (CopZ1)
ComponentsCoatomer subunit zeta-1
KeywordsSTRUCTURAL PROTEIN / Cancer / Dormant Cells / Human COPI / CopZ1
Function / homology
Function and homology information


COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / transport vesicle / intracellular protein transport / Golgi membrane / endoplasmic reticulum membrane / cytosol
Similarity search - Function
Beta-Lactamase - #60 / Coatomer subunit zeta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Coatomer subunit zeta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLunev, S. / Groves, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)1P20GM109091 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of truncated human coatomer protein complex subunit zeta 1 (Cop zeta 1).
Authors: Lunev, S. / Semmelink, M.F. / Xian, J.L. / Ma, K.Y. / Leenders, A.J. / Domling, A.S. / Shtutman, M. / Groves, M.R.
History
DepositionNov 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit zeta-1
B: Coatomer subunit zeta-1


Theoretical massNumber of molelcules
Total (without water)33,3902
Polymers33,3902
Non-polymers00
Water2,090116
1
A: Coatomer subunit zeta-1


Theoretical massNumber of molelcules
Total (without water)16,6951
Polymers16,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coatomer subunit zeta-1


Theoretical massNumber of molelcules
Total (without water)16,6951
Polymers16,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.360, 65.403, 37.273
Angle α, β, γ (deg.)90.00, 96.58, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 12 - 150 / Label seq-ID: 9 - 147

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles :
ID
1
2

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Components

#1: Protein Coatomer subunit zeta-1 / Zeta-1-coat protein / Zeta-1 COP


Mass: 16695.096 Da / Num. of mol.: 2 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPZ1, COPZ, CGI-120, HSPC181 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: P61923
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: Thin plates of rectangular shape
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 2.2 M DL-Malic acid 0.2 M Na Malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2016
Details: LN2 cooled double crystal monochromator and two horizontal deflecting and one vertical deflecting X-ray mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→56.03 Å / Num. obs: 33495 / % possible obs: 97.3 % / Redundancy: 3.0246 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.883 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HF6

2hf6


Resolution: 1.6→56.03 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.234 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1619 4.8 %RANDOM
Rwork0.21041 ---
obs0.21243 31877 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.047 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20.21 Å2
2---0.09 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.6→56.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 0 116 2340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192256
X-RAY DIFFRACTIONr_bond_other_d0.0020.022204
X-RAY DIFFRACTIONr_angle_refined_deg2.5691.9823044
X-RAY DIFFRACTIONr_angle_other_deg1.28435066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67325108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80415422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.911512
X-RAY DIFFRACTIONr_chiral_restr0.1870.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022524
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02496
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_it0.9230.9511110
X-RAY DIFFRACTIONr_mcbond_other0.9130.951109
X-RAY DIFFRACTIONr_mcangle_it1.3761.4231384
X-RAY DIFFRACTIONr_mcangle_other1.3771.4241385
X-RAY DIFFRACTIONr_scbond_it1.5731.1571146
X-RAY DIFFRACTIONr_scbond_other1.5731.1581147
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3661.6551661
X-RAY DIFFRACTIONr_long_range_B_refined3.52918.7659461
X-RAY DIFFRACTIONr_long_range_B_other3.51118.6089397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8444 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 113 -
Rwork0.268 2310 -
obs--96.69 %
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)
11.49050.22360.36922.02570.06082.7389-0.01910.02510.06480.02810.01110.0475-0.06290.05820.00790.0278-0.0049-0.00270.029-0.00720.006612.02190.272913.5597
23.6387-0.4915-0.03073.3418-0.00172.2423-0.00620.12460.1826-0.1538-0.0597-0.0526-0.0647-0.02020.06590.06670.0080.00550.0702-0.00650.024417.4591-25.0179-4.3407
31.9760.5035-0.24922.7652-0.45242.2269-0.0305-0.0325-0.11390.043-0.01070.02560.0982-0.05560.04120.0410.0093-0.01610.055-0.00180.03159.5089-32.63233.4194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 150
2X-RAY DIFFRACTION2B12 - 60
3X-RAY DIFFRACTION3B61 - 150

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