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- EMDB-0312: Structure of McrBC without DNA binding domains (Class 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-0312
TitleStructure of McrBC without DNA binding domains (Class 2)
Map data
Sample
  • Complex: McrB and McrC complex without DNA binding domains
    • Protein or peptide: 5-methylcytosine-specific restriction enzyme B
    • Protein or peptide: Protein McrC
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsAAA+ superfamily / restriction enzyme / DNA BINDING PROTEIN
Function / homology
Function and homology information


type IV site-specific deoxyribonuclease activity / restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA catabolic process / DNA restriction-modification system / endonuclease activity / GTPase activity ...type IV site-specific deoxyribonuclease activity / restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA catabolic process / DNA restriction-modification system / endonuclease activity / GTPase activity / GTP binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
5-methylcytosine restriction system component, bacterial / Type IV methyl-directed restriction enzyme EcoKMcrBC / McrBC 5-methylcytosine restriction system component / Type IV methyl-directed restriction enzyme EcoKMcrB subunit, DNA-binding domain / MrcB-like, N-terminal domain / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type IV methyl-directed restriction enzyme EcoKMcrB subunit / Type IV methyl-directed restriction enzyme EcoKMcrBC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsItoh Y / Nirwan N
CitationJournal: Nat Commun / Year: 2019
Title: Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC.
Authors: Nirwan N / Itoh Y / Singh P / Bandyopadhyay S / Vinothkumar KR / Amunts A / Saikrishnan K
History
DepositionOct 22, 2018-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hz6
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0312.png

Downloads & links

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Map

FileDownload / File: emd_0312.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 240 pix.
= 252. Å		1.05 Å/pix.
x 240 pix.
= 252. Å		1.05 Å/pix.
x 240 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.049755756 - 0.08978675
Average (Standard dev.)0.0006660792 (±0.0046914225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0500.0900.001

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Supplemental data

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Mask #1

Fileemd_0312_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_0312_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_0312_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 : McrB and McrC complex without DNA binding domains

EntireName: McrB and McrC complex without DNA binding domains
Components
  • Complex: McrB and McrC complex without DNA binding domains
    • Protein or peptide: 5-methylcytosine-specific restriction enzyme B
    • Protein or peptide: Protein McrC
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: McrB and McrC complex without DNA binding domains

SupramoleculeName: McrB and McrC complex without DNA binding domains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: The N-terminal DNA binding domain of McrB is truncated
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 510 KDa

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Macromolecule #1: 5-methylcytosine-specific restriction enzyme B

MacromoleculeName: 5-methylcytosine-specific restriction enzyme B / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 35.758492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKTESYCLE DALNDLFIPE TTIETILKRL TIKKNIILQG PPGVGKTFVA RRLAYLLTGE KAPQRVNMVQ FHQSYSYEDF IQGYRPNGV GFRRKDGIFY NFCQQAKEQP EKKYIFIIDE INRANLSKVF GEVMMLMEHD KRGENWSVPL TYSENDEERF Y VPENVYII ...String:
MSKTESYCLE DALNDLFIPE TTIETILKRL TIKKNIILQG PPGVGKTFVA RRLAYLLTGE KAPQRVNMVQ FHQSYSYEDF IQGYRPNGV GFRRKDGIFY NFCQQAKEQP EKKYIFIIDE INRANLSKVF GEVMMLMEHD KRGENWSVPL TYSENDEERF Y VPENVYII GLMNTADRSL AVVDYALRRR FSFIDIEPGF DTPQFRNFLL NKKAEPSFVE SLCQKMNELN QEISKEATIL GK GFRIGHS YFCCGLEDGT SPDTQWLNEI VMTDIAPLLE EYFFDDPYKQ QKWTNKLLGD SSGSHHHHHH

UniProtKB: Type IV methyl-directed restriction enzyme EcoKMcrB subunit

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Macromolecule #2: Protein McrC

MacromoleculeName: Protein McrC / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 40.643625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEQPVIPVRN IYYMLTYAWG YLQEIKQANL EAIPGNNLLD ILGYVLNKGV LQLSRRGLEL DYNPNTEIIP GIKGRIEFAK TIRGFHLNH GKTVSTFDML NEDTLANRII KSTLAILIKH EKLNSTIRDE ARSLYRKLPG ISTLHLTPQH FSYLNGGKNT R YYKFVISV ...String:
MEQPVIPVRN IYYMLTYAWG YLQEIKQANL EAIPGNNLLD ILGYVLNKGV LQLSRRGLEL DYNPNTEIIP GIKGRIEFAK TIRGFHLNH GKTVSTFDML NEDTLANRII KSTLAILIKH EKLNSTIRDE ARSLYRKLPG ISTLHLTPQH FSYLNGGKNT R YYKFVISV CKFIVNNSIP GQNKGHYRFY DFERNEKEMS LLYQKFLYEF CRRELTSANT TRSYLKWDAS SISDQSLNLL PR METDITI RSSEKILIVD AKYYKSIFSR RMGTEKFHSQ NLYQLMNYLW SLKPENGENI GGLLIYPHVD TAVKHRYKIN GFD IGLCTV NLGQEWPCIH QELLDIFDEY LK

UniProtKB: Type IV methyl-directed restriction enzyme EcoKMcrBC

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 3 / Number of copies: 6 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / 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: 6 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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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

Concentration4.0 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.1 MNaClsodium chloride
10.0 mMTris-HCltris(hydroxymethyl)aminomethane hydrochloride buffer
5.0 mMMgCl2Magnesium chloride
2.0 mMC10H17N6O13P35'-Guanylyl imidodiphosphate
GridModel: C-flat-2/2 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 3326 / Average exposure time: 8.0 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 771763
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0) / Number images used: 225201
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 74 / Target criteria: Cross-correlation coefficient
Output model

PDB-6hz6:
Structure of McrBC without DNA binding domains (Class 2)

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