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- PDB-3cjk: Crystal structure of the adduct HAH1-Cd(II)-MNK1. -

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Basic information

Entry
Database: PDB / ID: 3cjk
TitleCrystal structure of the adduct HAH1-Cd(II)-MNK1.
Components
  • Copper transport protein ATOX1
  • Copper-transporting ATPase 1
KeywordsMETAL TRANSPORT/HYDROLASE / HAH1 / ATP7A / ATP7B / Menkes disease / metal homeostasis / Chaperone / Copper / Copper transport / Ion transport / Metal-binding / Transport / Alternative splicing / ATP-binding / Cytoplasm / Disease mutation / Endoplasmic reticulum / Glycoprotein / Golgi apparatus / Hydrolase / Magnesium / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Transmembrane / METAL TRANSPORT-HYDROLASE COMPLEX
Function / homology
Function and homology information


peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / metallochaperone activity / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding ...peptidyl-lysine modification / epinephrine metabolic process / elastin biosynthetic process / positive regulation of response to wounding / metallochaperone activity / tryptophan metabolic process / cellular response to cobalt ion / Ion influx/efflux at host-pathogen interface / positive regulation of tyrosinase activity / copper-dependent protein binding / copper chaperone activity / cerebellar Purkinje cell differentiation / elastic fiber assembly / response to iron(III) ion / copper ion transmembrane transporter activity / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / positive regulation of melanin biosynthetic process / superoxide dismutase copper chaperone activity / cellular response to lead ion / pyramidal neuron development / copper ion export / copper ion import / copper ion homeostasis / copper ion transport / melanosome membrane / catecholamine metabolic process / serotonin metabolic process / detoxification of copper ion / norepinephrine metabolic process / trans-Golgi network transport vesicle / regulation of oxidative phosphorylation / T-helper cell differentiation / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / cartilage development / response to manganese ion / negative regulation of iron ion transmembrane transport / cellular response to antibiotic / skin development / hair follicle morphogenesis / pigmentation / dopamine metabolic process / lung alveolus development / response to zinc ion / cellular response to platelet-derived growth factor stimulus / positive regulation of catalytic activity / cell leading edge / blood vessel development / central nervous system neuron development / Detoxification of Reactive Oxygen Species / cuprous ion binding / Ion transport by P-type ATPases / microvillus / positive regulation of cell size / intracellular copper ion homeostasis / blood vessel remodeling / positive regulation of lamellipodium assembly / cellular response to copper ion / cellular response to cadmium ion / lactation / removal of superoxide radicals / mitochondrion organization / extracellular matrix organization / neuron projection morphogenesis / trans-Golgi network membrane / liver development / secretory granule / locomotory behavior / positive regulation of epithelial cell proliferation / female pregnancy / cellular response to iron ion / brush border membrane / cellular response to amino acid stimulus / trans-Golgi network / small GTPase binding / phagocytic vesicle membrane / late endosome / early endosome membrane / protein-folding chaperone binding / cellular response to hypoxia / basolateral plasma membrane / perikaryon / in utero embryonic development / response to oxidative stress / postsynaptic density / neuron projection / apical plasma membrane / copper ion binding / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / E1-E2 ATPase ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Copper transport protein ATOX1 / Copper-transporting ATPase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBanci, L. / Bertini, I. / Calderone, V. / Felli, I. / Della-Malva, N. / Pavelkova, A. / Rosato, A.
Citation
Journal: Biochem.J. / Year: 2009
Title: Copper(I)-mediated protein-protein interactions result from suboptimal interaction surfaces.
Authors: Banci, L. / Bertini, I. / Calderone, V. / Della-Malva, N. / Felli, I.C. / Neri, S. / Pavelkova, A. / Rosato, A.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: A NMR study of the interaction of a three-domain construct of ATP7A with copper(I) and copper(I)-HAH1: the interplay of domains.
Authors: Banci, L. / Bertini, I. / Cantini, F. / Chasapis, C. / Hadjiliadis, N. / Rosato, A.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: Structural basis for copper transfer by the metallochaperone for the Menkes/Wilson disease proteins.
Authors: Wernimont, A.K. / Huffman, D.L. / Lamb, A.L. / O'Halloran, T.V. / Rosenzweig, A.C.
History
DepositionMar 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Copper transport protein ATOX1
B: Copper-transporting ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8243
Polymers15,7122
Non-polymers1121
Water1,36976
1
A: Copper transport protein ATOX1


Theoretical massNumber of molelcules
Total (without water)7,3951
Polymers7,3951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Copper-transporting ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4302
Polymers8,3171
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.707, 55.274, 63.241
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 Copper transport protein ATOX1 / Metal transport protein ATX1


Mass: 7394.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATOX1, HAH1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00244
#2: Protein Copper-transporting ATPase 1 / Copper pump 1 / Menkes disease-associated protein


Mass: 8317.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP7A, MC1, MNK / Production host: Escherichia coli (E. coli) / References: UniProt: Q04656, Cu2+-exporting ATPase
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 0.1 M sodium citrate, 20% PEG-6000, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97245 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2008 / Details: Silicon toroidal mirror coated with Rhodium
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97245 Å / Relative weight: 1
ReflectionResolution: 1.8→26.3 Å / Num. all: 16071 / Num. obs: 16071 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 5.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / Num. unique all: 2307 / Rsym value: 0.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FE0

1fe0


Resolution: 1.8→26.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.404 / SU ML: 0.103
Isotropic thermal model: Isotropic except Cd2+ which was refined anisotropically
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28253 1454 9 %RANDOM
Rwork0.22569 ---
all0.23075 14615 --
obs0.23075 14615 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.744 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.57 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 1 76 1170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221107
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.9631493
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91626.51243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97915211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.293152
X-RAY DIFFRACTIONr_chiral_restr0.1410.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02784
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_it1.3931.5706
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43621147
X-RAY DIFFRACTIONr_scbond_it3.613401
X-RAY DIFFRACTIONr_scangle_it5.7294.5346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free9.53331
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 122 -
Rwork0.271 1049 -
obs--100 %

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