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- PDB-6m97: Crystal structure of the high-affinity copper transporter Ctr1 -

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Basic information

Entry
Database: PDB / ID: 6m97
TitleCrystal structure of the high-affinity copper transporter Ctr1
ComponentsChimera protein of High affinity copper uptake protein 1 and Soluble cytochrome b562
KeywordsTRANSPORT PROTEIN / Membrane proteins / Ion transporters / Ion channels.
Function / homology
Function and homology information


copper ion transmembrane transporter activity / intracellular copper ion homeostasis / electron transfer activity / periplasmic space / iron ion binding / heme binding / membrane
Similarity search - Function
Ctr copper transporter / Ctr copper transporter family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / Copper transport protein / Soluble cytochrome b562
Similarity search - Component
Biological speciesSalmo salar (Atlantic salmon)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.03 Å
AuthorsRen, F. / Yuan, P.
CitationJournal: Nat Commun / Year: 2019
Title: X-ray structures of the high-affinity copper transporter Ctr1.
Authors: Ren, F. / Logeman, B.L. / Zhang, X. / Liu, Y. / Thiele, D.J. / Yuan, P.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera protein of High affinity copper uptake protein 1 and Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4274
Polymers26,2721
Non-polymers4,1543
Water0
1
A: Chimera protein of High affinity copper uptake protein 1 and Soluble cytochrome b562
hetero molecules

A: Chimera protein of High affinity copper uptake protein 1 and Soluble cytochrome b562
hetero molecules

A: Chimera protein of High affinity copper uptake protein 1 and Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,28112
Polymers78,8173
Non-polymers12,4639
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6280 Å2
ΔGint-161 kcal/mol
Surface area35170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.850, 73.850, 410.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2002-

TBR

21A-2002-

TBR

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Components

#1: Protein Chimera protein of High affinity copper uptake protein 1 and Soluble cytochrome b562 / / high affinity copper uptake protein 1 isoform X1 / Cytochrome b-562 / high affinity copper uptake ...high affinity copper uptake protein 1 isoform X1 / Cytochrome b-562 / high affinity copper uptake protein 1 isoform X1


Mass: 26272.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon), (gene. exp.) Escherichia coli (E. coli)
Gene: COPT1, copt1, cybC / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: C0HAK2, UniProt: P0ABE7
#2: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br12Ta6
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 4.27 Å3/Da / Density % sol: 71.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM zinc acetate, 50 mM sodium cacodylate pH 5.9, and 26% PEG 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2546 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2546 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 8991 / % possible obs: 99.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.057 / Net I/σ(I): 16.8
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 1.578 / Num. unique obs: 890 / CC1/2: 0.747 / Rpim(I) all: 0.732

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.03→20 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.851 / SU B: 46.178 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.585 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33231 678 9.8 %RANDOM
Rwork0.28048 ---
obs0.2854 6233 77.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 74.442 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.31 Å20 Å2
2---0.62 Å20 Å2
3---2 Å2
Refinement stepCycle: 1 / Resolution: 3.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 37 0 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191721
X-RAY DIFFRACTIONr_bond_other_d0.0020.021580
X-RAY DIFFRACTIONr_angle_refined_deg1.3152.1052587
X-RAY DIFFRACTIONr_angle_other_deg0.88633633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47524.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.59157
X-RAY DIFFRACTIONr_chiral_restr0.0550.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
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_it0.7064.409827
X-RAY DIFFRACTIONr_mcbond_other0.7064.409826
X-RAY DIFFRACTIONr_mcangle_it1.2626.611025
X-RAY DIFFRACTIONr_mcangle_other1.2616.6091026
X-RAY DIFFRACTIONr_scbond_it0.5914.591889
X-RAY DIFFRACTIONr_scbond_other0.5824.417818
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1056.611203
X-RAY DIFFRACTIONr_long_range_B_refined2.76652.2931881
X-RAY DIFFRACTIONr_long_range_B_other2.76552.2811882
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.031→3.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.832 3 -
Rwork0.335 43 -
obs--7.3 %
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)
14.92790.7639-2.63792.0702-0.05954.2864-0.03490.19150.4494-0.3030.0634-0.0721-0.7384-0.1041-0.02840.2221-0.0045-0.04090.0080.01450.0711-36.4537-9.257143.7967
24.3769-0.231-1.82096.24091.43189.9184-0.12170.2196-0.2013-0.6075-0.0138-0.2251-0.2017-0.33380.13550.3238-0.04850.04010.35270.05040.2771-21.5733-11.15195.3567
318.1849.086215.22017.24566.091713.64720.0201-0.0877-0.18160.04010.0124-0.0866-0.0686-0.1473-0.03250.31960.02160.02630.3096-0.01390.3805-18.08374.63087.1156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 182
2X-RAY DIFFRACTION2A1002 - 1105
3X-RAY DIFFRACTION3A2001 - 2002

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