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- PDB-4h4k: Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex -

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Basic information

Entry
Database: PDB / ID: 4h4k
TitleStructure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex
Components(CRISPR system Cmr subunit ...) x 2
KeywordsRNA BINDING PROTEIN / Ferredoxin / Palm / RAMP / Repeat Associated Mysterious Protein / Polymerase / Nuclease / RNA-interference / Cmr proteins CRISPR RNA
Function / homology
Function and homology information


defense response to virus / nucleotide binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #2940 / Immunoglobulin-like - #4350 / Carboxypeptidase Inhibitor; Chain A - #70 / CRISPR-Cas system, Cmr2 subunit, D2 domain, helical bundle / CRISPR-Cas system, Cmr2 subunit, D4 domain, six-helix bundle / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / : / : / CRISPR RNA silencing complex Cmr2 subunit, first helical domain / CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain ...Alpha-Beta Plaits - #2940 / Immunoglobulin-like - #4350 / Carboxypeptidase Inhibitor; Chain A - #70 / CRISPR-Cas system, Cmr2 subunit, D2 domain, helical bundle / CRISPR-Cas system, Cmr2 subunit, D4 domain, six-helix bundle / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / : / : / CRISPR RNA silencing complex Cmr2 subunit, first helical domain / CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain / CRISPR-associated protein, TM1793 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / Carboxypeptidase Inhibitor; Chain A / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / CRISPR-associated protein Cmr2, N-terminal / : / CRISPR RNA silencing complex Cmr2 subunit, second helical domain / GGDEF domain profile. / GGDEF domain / Reverse transcriptase/Diguanylate cyclase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Arc Repressor Mutant, subunit A / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CRISPR system Cmr subunit Cmr2 / CRISPR system Cmr subunit Cmr3
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.804 Å
AuthorsShao, Y. / Cocozaki, A.I. / Ramia, N.F. / Terns, R.M. / Terns, M.P. / Li, H.
CitationJournal: Structure / Year: 2013
Title: Structure of the cmr2-cmr3 subcomplex of the cmr RNA silencing complex.
Authors: Shao, Y. / Cocozaki, A.I. / Ramia, N.F. / Terns, R.M. / Terns, M.P. / Li, H.
History
DepositionSep 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Mar 30, 2016Group: Other
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_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.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_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

Downloads & links

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Assembly

Deposited unit
A: CRISPR system Cmr subunit Cmr3
C: CRISPR system Cmr subunit Cmr2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4476
Polymers116,8282
Non-polymers6194
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-32 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.523, 135.958, 189.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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CRISPR system Cmr subunit ... , 2 types, 2 molecules AC

#1: Protein CRISPR system Cmr subunit Cmr3 / CRISPR type III-B/RAMP module-associated protein Cmr3


Mass: 36366.379 Da / Num. of mol.: 1 / Fragment: Cmr3 (unp residues 1-322) / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: cmr3, PF1128 / Plasmid: PET200D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8U1S7
#2: Protein CRISPR system Cmr subunit Cmr2 / CRISPR-associated protein Cas10/Cmr2 / subtype III-B


Mass: 80461.828 Da / Num. of mol.: 1 / Fragment: Cmr2dHD (unp residues 215-871) / Mutation: dHD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: cmr2, PF1129 / Plasmid: PET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8U1S6

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Non-polymers , 4 types, 5 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% Polyethylene Glycol (PEG1500) , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303.15K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.0456 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2010
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0456 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 32825 / Num. obs: 32764 / % possible obs: 99.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5
Reflection shellResolution: 2.8→2.85 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.804→36.833 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 1909 6.11 %RANDOM
Rwork0.2143 ---
obs0.2185 31226 94.95 %-
all-32825 --
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.57 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.8455 Å2-0 Å2-0 Å2
2---4.5081 Å20 Å2
3----5.3374 Å2
Refinement stepCycle: LAST / Resolution: 2.804→36.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6979 0 34 1 7014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087172
X-RAY DIFFRACTIONf_angle_d1.1469682
X-RAY DIFFRACTIONf_dihedral_angle_d19.632714
X-RAY DIFFRACTIONf_chiral_restr0.071075
X-RAY DIFFRACTIONf_plane_restr0.0041200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8039-2.8740.46521080.36581727X-RAY DIFFRACTION79
2.874-2.95170.37441240.31081871X-RAY DIFFRACTION86
2.9517-3.03850.35271290.27971937X-RAY DIFFRACTION89
3.0385-3.13650.3431300.26761977X-RAY DIFFRACTION92
3.1365-3.24860.30671380.22962111X-RAY DIFFRACTION96
3.2486-3.37860.30951380.23772101X-RAY DIFFRACTION96
3.3786-3.53220.29951370.22392138X-RAY DIFFRACTION97
3.5322-3.71830.29681400.2062140X-RAY DIFFRACTION98
3.7183-3.9510.27491380.19782159X-RAY DIFFRACTION98
3.951-4.25560.26551430.18422196X-RAY DIFFRACTION99
4.2556-4.68310.2421430.17072186X-RAY DIFFRACTION99
4.6831-5.3590.26421440.18712219X-RAY DIFFRACTION100
5.359-6.7450.30921460.23782238X-RAY DIFFRACTION100
6.745-36.83590.24781510.21022317X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 36.4336 Å / Origin y: -46.5134 Å / Origin z: 28.7962 Å
111213212223313233
T0.2515 Å20.0499 Å20.0433 Å2-0.2152 Å2-0.11 Å2--0.2163 Å2
L0.3017 °2-0.1838 °2-0.0319 °2-0.4413 °20.1202 °2--0.332 °2
S0.0306 Å °-0.0704 Å °0.0971 Å °-0.0004 Å °-0.0991 Å °0.0982 Å °-0.0742 Å °-0.0686 Å °-0.3269 Å °
Refinement TLS groupSelection details: all

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