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- EMDB-21540: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP... -

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Basic information

Entry
Database: EMDB / ID: EMD-21540
TitleHolocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP
Map dataHolocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP
Sample
  • Complex: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP
    • Protein or peptide: Ribonucleoside-diphosphate reductase 1 subunit alphaRibonucleotide reductase
    • Protein or peptide: Ribonucleoside-diphosphate reductase 1 subunit betaRibonucleotide reductase
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MU-OXO-DIIRON
  • Ligand: water
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / iron ion binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / iron ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
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 / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase 1 subunit alpha / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKang G / Taguchi A / Stubbe J / Drennan C
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2020
Title: Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex.
Authors: Gyunghoon Kang / Alexander T Taguchi / JoAnne Stubbe / Catherine L Drennan /
Abstract: Ribonucleotide reductases (RNRs) are a diverse family of enzymes that are alone capable of generating 2'-deoxynucleotides de novo and are thus critical in DNA biosynthesis and repair. The nucleotide ...Ribonucleotide reductases (RNRs) are a diverse family of enzymes that are alone capable of generating 2'-deoxynucleotides de novo and are thus critical in DNA biosynthesis and repair. The nucleotide reduction reaction in all RNRs requires the generation of a transient active site thiyl radical, and in class I RNRs, this process involves a long-range radical transfer between two subunits, α and β. Because of the transient subunit association, an atomic resolution structure of an active α2β2 RNR complex has been elusive. We used a doubly substituted β2, E52Q/(2,3,5)-trifluorotyrosine122-β2, to trap wild-type α2 in a long-lived α2β2 complex. We report the structure of this complex by means of cryo-electron microscopy to 3.6-angstrom resolution, allowing for structural visualization of a 32-angstrom-long radical transfer pathway that affords RNR activity.
History
DepositionMar 11, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseApr 8, 2020-
UpdateMay 6, 2020-
Current statusMay 6, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0214
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0214
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w4x
  • Surface level: 0.0214
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21540.png

Downloads & links

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Map

FileDownload / File: emd_21540.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHolocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.0214 / Movie #1: 0.0214
Minimum - Maximum-0.10288604 - 0.1401187
Average (Standard dev.)0.0000246463 (±0.005196847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.160254.160254.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ336336336
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1030.1400.000

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Supplemental data

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Half map: #1

Fileemd_21540_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_21540_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Holocomplex of E. coli class Ia ribonucleotide reductase with GDP...

EntireName: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP
Components
  • Complex: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP
    • Protein or peptide: Ribonucleoside-diphosphate reductase 1 subunit alphaRibonucleotide reductase
    • Protein or peptide: Ribonucleoside-diphosphate reductase 1 subunit betaRibonucleotide reductase
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MU-OXO-DIIRON
  • Ligand: water

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Supramolecule #1: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP...

SupramoleculeName: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Ribonucleoside-diphosphate reductase 1 subunit alpha

MacromoleculeName: Ribonucleoside-diphosphate reductase 1 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonucleoside-diphosphate reductase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 85.877086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNQNLLVTKR DGSTERINLD KIHRVLDWAA EGLHNVSISQ VELRSHIQFY DGIKTSDIHE TIIKAAADLI SRDAPDYQYL AARLAIFHL RKKAYGQFEP PALYDHVVKM VEMGKYDNHL LEDYTEEEFK QMDTFIDHDR DMTFSYAAVK QLEGKYLVQN R VTGEIYES ...String:
MNQNLLVTKR DGSTERINLD KIHRVLDWAA EGLHNVSISQ VELRSHIQFY DGIKTSDIHE TIIKAAADLI SRDAPDYQYL AARLAIFHL RKKAYGQFEP PALYDHVVKM VEMGKYDNHL LEDYTEEEFK QMDTFIDHDR DMTFSYAAVK QLEGKYLVQN R VTGEIYES AQFLYILVAA CLFSNYPRET RLQYVKRFYD AVSTFKISLP TPIMSGVRTP TRQFSSCVLI ECGDSLDSIN AT SSAIVKY VSQRAGIGIN AGRIRALGSP IRGGEAFHTG CIPFYKHFQT AVKSCSQGGV RGGAATLFYP MWHLEVESLL VLK NNRGVE GNRVRHMDYG VQINKLMYTR LLKGEDITLF SPSDVPGLYD AFFADQEEFE RLYTKYEKDD SIRKQRVKAV ELFS LMMQE RASTGRIYIQ NVDHCNTHSP FDPAIAPVRQ SNLCLEIALP TKPLNDVNDE NGEIALCTLS AFNLGAINNL DELEE LAIL AVRALDALLD YQDYPIPAAK RGAMGRRTLG IGVINFAYYL AKHGKRYSDG SANNLTHKTF EAIQYYLLKA SNELAK EQG ACPWFNETTY AKGILPIDTY KKDLDTIANE PLHYDWEALR ESIKTHGLRN STLSALMPSE TSSQISNATN GIEPPRG YV SIKASKDGIL RQVVPDYEHL HDAYELLWEM PGNDGYLQLV GIMQKFIDQS ISANTNYDPS RFPSGKVPMQ QLLKDLLT A YKFGVKTLYY QNTRDGAEDA QDDLVPSIQD DGCESGACKI

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Macromolecule #2: Ribonucleoside-diphosphate reductase 1 subunit beta

MacromoleculeName: Ribonucleoside-diphosphate reductase 1 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonucleoside-diphosphate reductase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 43.611039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR PEQVDVSRDR IDYQALPEHE KHIFISNLKY QTLLDSIQG RSPNVALLPL ISIPELETWV ETWAFSETIH SRS(FY3)THIIRN IVNDPSVVFD DIVTNEQIQK RAEGISS YY DELIEMTSYW ...String:
MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR PEQVDVSRDR IDYQALPEHE KHIFISNLKY QTLLDSIQG RSPNVALLPL ISIPELETWV ETWAFSETIH SRS(FY3)THIIRN IVNDPSVVFD DIVTNEQIQK RAEGISS YY DELIEMTSYW HLLGEGTHTV NGKTVTVSLR ELKKKLYLCL MSVNALEAIR FYVSFACSFA FAERELMEGN AKIIRLIA R DEALHLTGTQ HMLNLLRSGA DDPEMAEIAE ECKQECYDLF VQAAQQEKDW ADYLFRDGSM IGLNKDILCQ YVEYITNIR MQAVGLDLPF QTRSNPIPWI NTWLVSDNVQ VAPQEVEVSS YLVGQIDSEV DTDDLSNFQL

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Macromolecule #3: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Macromolecule #6: MU-OXO-DIIRON

MacromoleculeName: MU-OXO-DIIRON / type: ligand / ID: 6 / Number of copies: 2 / Formula: FEO
Molecular weightTheoretical: 127.689 Da
Chemical component information

ChemComp-FEO:
MU-OXO-DIIRON

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4.5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 2 / Number real images: 6238 / Average exposure time: 6.0 sec. / Average electron dose: 47.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.0)
Startup modelType of model: INSILICO MODEL / In silico model: De novo 3D model generation in Relion
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 80386
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5cnv

RefinementSpace: REAL
Output model

PDB-6w4x:
Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP

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