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- PDB-2wgh: Human Ribonucleotide reductase R1 subunit (RRM1) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2wgh
TitleHuman Ribonucleotide reductase R1 subunit (RRM1) in complex with dATP and Mg.
ComponentsRIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE SUBUNITRibonucleotide reductase
KeywordsOXIDOREDUCTASE / DNA REPLICATION / ALLOSTERIC ENZYME / NUCLEOTIDE-BINDING / CYTOPLASM / ATP-BINDING / POLYMORPHISM
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / positive regulation of G0 to G1 transition / mitochondrial DNA replication / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor ...ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / positive regulation of G0 to G1 transition / mitochondrial DNA replication / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / Interconversion of nucleotide di- and triphosphates / deoxyribonucleotide biosynthetic process / protein heterotetramerization / DNA synthesis involved in DNA repair / response to ionizing radiation / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / cell projection / male gonad development / disordered domain specific binding / retina development in camera-type eye / nuclear envelope / DNA repair / neuronal cell body / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal ...Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase large subunit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWelin, R.M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Welin, R.M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kragh-Nielsen, T. / Kotzsch, A. / Kotenyova, T. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Wisniewska, M. / Nordlund, P.
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization.
Authors: James Wesley Fairman / Sanath Ranjan Wijerathna / Md Faiz Ahmad / Hai Xu / Ryo Nakano / Shalini Jha / Jay Prendergast / R Martin Welin / Susanne Flodin / Annette Roos / Pär Nordlund / ...Authors: James Wesley Fairman / Sanath Ranjan Wijerathna / Md Faiz Ahmad / Hai Xu / Ryo Nakano / Shalini Jha / Jay Prendergast / R Martin Welin / Susanne Flodin / Annette Roos / Pär Nordlund / Zongli Li / Thomas Walz / Chris Godfrey Dealwis /
Abstract: Ribonucleotide reductase (RR) is an α(n)β(n) (RR1-RR2) complex that maintains balanced dNTP pools by reducing NDPs to dNDPs. RR1 is the catalytic subunit, and RR2 houses the free radical required ...Ribonucleotide reductase (RR) is an α(n)β(n) (RR1-RR2) complex that maintains balanced dNTP pools by reducing NDPs to dNDPs. RR1 is the catalytic subunit, and RR2 houses the free radical required for catalysis. RR is allosterically regulated by its activator ATP and its inhibitor dATP, which regulate RR activity by inducing oligomerization of RR1. Here, we report the first X-ray structures of human RR1 bound to TTP alone, dATP alone, TTP-GDP, TTP-ATP, and TTP-dATP. These structures provide insights into regulation of RR by ATP or dATP. At physiological dATP concentrations, RR1 forms inactive hexamers. We determined the first X-ray structure of the RR1-dATP hexamer and used single-particle electron microscopy to visualize the α(6)-ββ'-dATP holocomplex. Site-directed mutagenesis and functional assays confirm that hexamerization is a prerequisite for inhibition by dATP. Our data indicate a mechanism for regulating RR activity by dATP-induced oligomerization.
History
DepositionApr 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE SUBUNIT
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,4517
Polymers154,3282
Non-polymers1,1235
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34.1 kcal/mol
Surface area46710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.950, 129.310, 76.670
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE SUBUNIT / Ribonucleotide reductase / RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT / RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M1 / ...RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT / RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M1 / RIBONUCLEOTIDE REDUCTASE LARGE SUBUNIT


Mass: 77163.977 Da / Num. of mol.: 2 / Fragment: R1 SUBUNIT, RESIDUES 75-742
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION / Plasmid: PNIC-CH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) R3 PRARE
References: UniProt: P23921, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NATIVE SEQUENCE CONSIST OF 792 AMINO ACIDS AND OUR CONSTRUCT CONTAIN THE NATIVE RESIDUES 75-742 ...THE NATIVE SEQUENCE CONSIST OF 792 AMINO ACIDS AND OUR CONSTRUCT CONTAIN THE NATIVE RESIDUES 75-742 WITH AN ADDITIONAL C-TERMINAL HEXAHISTIDINE TAIL -AHHHHHH.

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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: 2.21 Å3/Da / Density % sol: 43.99 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→49 Å / Num. obs: 56722 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZYZ

1zyz


Resolution: 2.3→48.85 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.765 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25762 2837 5 %RANDOM
Rwork0.19222 ---
obs0.1955 53884 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.629 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å23.99 Å2
2---2.92 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10357 0 68 231 10656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210658
X-RAY DIFFRACTIONr_bond_other_d0.0010.027205
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.96614448
X-RAY DIFFRACTIONr_angle_other_deg0.952317583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72251297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28324.585482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.692151871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2631552
X-RAY DIFFRACTIONr_chiral_restr0.0940.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022093
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_it0.7381.56478
X-RAY DIFFRACTIONr_mcbond_other0.1611.52625
X-RAY DIFFRACTIONr_mcangle_it1.367210454
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.14734180
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4074.53993
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 207 -
Rwork0.259 3916 -
obs--100 %

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