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- PDB-8rnz: Metal-binding domain 3 of copper-transporting ATPase RAN1 from Ar... -

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Basic information

Entry
Database: PDB / ID: 8rnz
TitleMetal-binding domain 3 of copper-transporting ATPase RAN1 from Arabidopsis thaliana
ComponentsCopper-transporting ATPase RAN1
KeywordsMETAL BINDING PROTEIN / transport protein / copper transport
Function / homology
Function and homology information


response to ethylene / ethylene-activated signaling pathway / regulation of stomatal movement / P-type Cu+ transporter / P-type monovalent copper transporter activity / trans-Golgi network / endosome / copper ion binding / Golgi apparatus / ATP hydrolysis activity ...response to ethylene / ethylene-activated signaling pathway / regulation of stomatal movement / P-type Cu+ transporter / P-type monovalent copper transporter activity / trans-Golgi network / endosome / copper ion binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / 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 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain ...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 / 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
Similarity search - Domain/homology
Copper-transporting ATPase RAN1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMinges, A. / Dluhosch, D. / Groth, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)267205415/CRC 1208 Germany
Citation
Journal: To Be Published / Year: 2025
Title: Exploring the Role of Individual Metal Binding Domains (MBDs) in Soluble and Membrane-bound Copper Chaperones for Metal Transport and Delivery to the ETR1 Ethylene Receptor in Arabidopsis thaliana
Authors: Dluhosch, D. / Kersten, L.S. / Minges, A. / Smits, S.H.J. / Gohlke, H. / Groth, G.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: DIALS: implementation and evaluation of a new integration package.
Authors: Winter, G. / Waterman, D.G. / Parkhurst, J.M. / Brewster, A.S. / Gildea, R.J. / Gerstel, M. / Fuentes-Montero, L. / Vollmar, M. / Michels-Clark, T. / Young, I.D. / Sauter, N.K. / Evans, G.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The CCP4 suite: integrative software for macromolecular crystallography.
Authors: Agirre, J. / Atanasova, M. / Bagdonas, H. / Ballard, C.B. / Basle, A. / Beilsten-Edmands, J. / Borges, R.J. / Brown, D.G. / Burgos-Marmol, J.J. / Berrisford, J.M. / Bond, P.S. / Caballero, I. ...Authors: Agirre, J. / Atanasova, M. / Bagdonas, H. / Ballard, C.B. / Basle, A. / Beilsten-Edmands, J. / Borges, R.J. / Brown, D.G. / Burgos-Marmol, J.J. / Berrisford, J.M. / Bond, P.S. / Caballero, I. / Catapano, L. / Chojnowski, G. / Cook, A.G. / Cowtan, K.D. / Croll, T.I. / Debreczeni, J.E. / Devenish, N.E. / Dodson, E.J. / Drevon, T.R. / Emsley, P. / Evans, G. / Evans, P.R. / Fando, M. / Foadi, J. / Fuentes-Montero, L. / Garman, E.F. / Gerstel, M. / Gildea, R.J. / Hatti, K. / Hekkelman, M.L. / Heuser, P. / Hoh, S.W. / Hough, M.A. / Jenkins, H.T. / Jimenez, E. / Joosten, R.P. / Keegan, R.M. / Keep, N. / Krissinel, E.B. / Kolenko, P. / Kovalevskiy, O. / Lamzin, V.S. / Lawson, D.M. / Lebedev, A.A. / Leslie, A.G.W. / Lohkamp, B. / Long, F. / Maly, M. / McCoy, A.J. / McNicholas, S.J. / Medina, A. / Millan, C. / Murray, J.W. / Murshudov, G.N. / Nicholls, R.A. / Noble, M.E.M. / Oeffner, R. / Pannu, N.S. / Parkhurst, J.M. / Pearce, N. / Pereira, J. / Perrakis, A. / Powell, H.R. / Read, R.J. / Rigden, D.J. / Rochira, W. / Sammito, M. / Sanchez Rodriguez, F. / Sheldrick, G.M. / Shelley, K.L. / Simkovic, F. / Simpkin, A.J. / Skubak, P. / Sobolev, E. / Steiner, R.A. / Stevenson, K. / Tews, I. / Thomas, J.M.H. / Thorn, A. / Valls, J.T. / Uski, V. / Uson, I. / Vagin, A. / Velankar, S. / Vollmar, M. / Walden, H. / Waterman, D. / Wilson, K.S. / Winn, M.D. / Winter, G. / Wojdyr, M. / Yamashita, K.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2006
Title: The Buccaneer software for automated model building. 1. Tracing protein chains.
Authors: Cowtan, K.
History
DepositionJan 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper-transporting ATPase RAN1
B: Copper-transporting ATPase RAN1


Theoretical massNumber of molelcules
Total (without water)23,0402
Polymers23,0402
Non-polymers00
Water1,44180
1
A: Copper-transporting ATPase RAN1


Theoretical massNumber of molelcules
Total (without water)11,5201
Polymers11,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Copper-transporting ATPase RAN1


Theoretical massNumber of molelcules
Total (without water)11,5201
Polymers11,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.755, 51.481, 62.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 51 through 54 or resid 56...
d_2ens_1(chain "B" and (resid 51 through 54 or resid 56...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUVALVALAA51 - 5451 - 54
d_12GLNGLNPHEPHEAA56 - 5756 - 57
d_13LEULEUASPASPAA59 - 6059 - 60
d_14ILEILEPROPROAA62 - 7262 - 72
d_15VALVALSERSERAA74 - 7774 - 77
d_16SERSERLYSLYSAA79 - 9379 - 93
d_17ARGARGMETMETAA95 - 9795 - 97
d_21LEULEUVALVALBB51 - 5451 - 54
d_22GLNGLNPHEPHEBB56 - 5756 - 57
d_23LEULEUASPASPBB59 - 6059 - 60
d_24ILEILEPROPROBB62 - 7262 - 72
d_25VALVALSERSERBB74 - 7774 - 77
d_26SERSERLYSLYSBB79 - 9379 - 93
d_27ARGARGMETMETBB95 - 9795 - 97

NCS oper: (Code: givenMatrix: (-0.978397376051, 0.0447928875603, -0.201822129017), (-0.0192830346096, -0.991762143824, -0.126633386809), (-0.205831822401, -0.120006030276, 0.971201221985)Vector: -4. ...NCS oper: (Code: given
Matrix: (-0.978397376051, 0.0447928875603, -0.201822129017), (-0.0192830346096, -0.991762143824, -0.126633386809), (-0.205831822401, -0.120006030276, 0.971201221985)
Vector: -4.16897478025, -26.3679286567, -12.5095471718)

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Components

#1: Protein Copper-transporting ATPase RAN1 / Protein HEAVY METAL ATPASE 7 / Protein RESPONSIVE TO ANTAGONIST 1


Mass: 11519.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAN1, HMA7, At5g44790, K23L20.14, T19K24.18 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9S7J8, P-type Cu+ transporter
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.82 Å3/Da / Density % sol: 34.4 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: precipitant: 200 mM sodium chloride, 100 mM MES pH 6.5, 10% (w/v) PEG 4000 protein solution: 4.8 mg/mL protein, 300 mM sodium chloride, 50 mM HEPES pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 15, 2023 / Details: Toroidal mirror
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.98→51.48 Å / Num. obs: 22108 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.35 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1204 / Rpim(I) all: 0.04984 / Rrim(I) all: 0.1306 / Net I/σ(I): 5.81
Reflection shellResolution: 1.98→2.08 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.5585 / Mean I/σ(I) obs: 0.74 / Num. unique obs: 1670 / CC1/2: 0.836 / CC star: 0.954 / Rpim(I) all: 0.2279 / Rrim(I) all: 0.6044 / % possible all: 99.24

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Processing

Software
NameVersionClassification
PHENIX1.21_5190refinement
MxCuBE3data collection
DIALS3.17.0data reduction
DIALS3.17.0data scaling
PHASER2.8.3phasing
BUCCANEER1.6.12model building
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→51.48 Å / SU ML: 0.3275 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.0095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 1043 4.72 %
Rwork0.1922 21042 -
obs0.1942 22085 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.42 Å2
Refinement stepCycle: LAST / Resolution: 1.98→51.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 0 80 1293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481242
X-RAY DIFFRACTIONf_angle_d0.62551674
X-RAY DIFFRACTIONf_chiral_restr0.0463195
X-RAY DIFFRACTIONf_plane_restr0.0058223
X-RAY DIFFRACTIONf_dihedral_angle_d12.3878474
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.687703311822 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.080.35871210.32363023X-RAY DIFFRACTION99.34
2.08-2.210.32941610.27732993X-RAY DIFFRACTION100
2.22-2.390.29441680.24262993X-RAY DIFFRACTION99.97
2.39-2.630.25271500.22773000X-RAY DIFFRACTION99.94
2.63-3.010.27311370.19483045X-RAY DIFFRACTION99.97
3.01-3.790.1951670.17452961X-RAY DIFFRACTION99.84
3.79-51.480.20171390.1493027X-RAY DIFFRACTION99.69

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