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- PDB-5xh6: Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR varia... -

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Basic information

Entry
Database: PDB / ID: 5xh6
TitleCrystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM)
Components
  • CRISPR-associated endonuclease Cpf1
  • Non-target DNA strand
  • Target DNA strand
  • crRNA
KeywordsHYDROLASE/RNA/DNA / nuclease / HYDROLASE-RNA-DNA complex
Function / homology
Function and homology information


Bacillus subtilis ribonuclease / Bacillus subtilis ribonuclease activity / deoxyribonuclease I / deoxyribonuclease I activity / defense response to virus / lyase activity / DNA binding / RNA binding
Similarity search - Function
CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas12a
Similarity search - Component
Biological speciesAcidaminococcus sp.
Acidaminococcus sp. BV3L6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNishimasu, H. / Yamano, T. / Ishitani, R. / Nureki, O.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1
Authors: Nishimasu, H. / Yamano, T. / Gao, L. / Zhang, F. / Ishitani, R. / Nureki, O.
History
DepositionApr 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cpf1
B: crRNA
C: Target DNA strand
D: Non-target DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,24728
Polymers178,9794
Non-polymers1,26824
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21530 Å2
ΔGint-120 kcal/mol
Surface area63490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.162, 133.676, 199.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain Target DNA strand


Mass: 10434.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA (30-MER) / Source: (synth.) Acidaminococcus sp. BV3L6 (bacteria)
#4: DNA chain Non-target DNA strand


Mass: 3003.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*AP*TP*A)-3') / Source: (synth.) Acidaminococcus sp. BV3L6 (bacteria)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein CRISPR-associated endonuclease Cpf1 / AsCpf1


Mass: 151784.391 Da / Num. of mol.: 1 / Mutation: S542R, K548V, N552R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus sp. (strain BV3L6) (bacteria)
Strain: BV3L6 / Gene: cpf1, HMPREF1246_0236 / Production host: Escherichia coli (E. coli)
References: UniProt: U2UMQ6, Hydrolases; Acting on ester bonds
#2: RNA chain crRNA


Mass: 13756.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA (40-MER) / Source: (synth.) Acidaminococcus sp. BV3L6 (bacteria)

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Non-polymers , 4 types, 683 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 7-10% PEG 3350, 100mM sodium acetate, pH 4.5, 10% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.99 Å / Num. obs: 143997 / % possible obs: 98.2 % / Redundancy: 6.6 % / Net I/σ(I): 17.1
Reflection shellResolution: 2→2.0227 Å / CC1/2: 0.813 / Rpim(I) all: 0.396

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B43
Resolution: 2→39.99 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2099 7064 4.91 %
Rwork0.175 --
obs0.1767 143851 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10378 1639 78 659 12754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712595
X-RAY DIFFRACTIONf_angle_d0.84317388
X-RAY DIFFRACTIONf_dihedral_angle_d17.4857368
X-RAY DIFFRACTIONf_chiral_restr0.051957
X-RAY DIFFRACTIONf_plane_restr0.0051958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.33272360.27244535X-RAY DIFFRACTION98
2.0227-2.04650.30852460.24854468X-RAY DIFFRACTION98
2.0465-2.07150.28382420.23864562X-RAY DIFFRACTION98
2.0715-2.09770.26992240.23374516X-RAY DIFFRACTION98
2.0977-2.12530.26422460.23294490X-RAY DIFFRACTION98
2.1253-2.15440.28612210.22364310X-RAY DIFFRACTION94
2.1544-2.18520.27912280.21544286X-RAY DIFFRACTION93
2.1852-2.21780.23022600.20094476X-RAY DIFFRACTION98
2.2178-2.25250.24742150.18984581X-RAY DIFFRACTION99
2.2525-2.28940.24872140.19224565X-RAY DIFFRACTION98
2.2894-2.32890.23432560.18184531X-RAY DIFFRACTION99
2.3289-2.37120.22412570.18814574X-RAY DIFFRACTION99
2.3712-2.41680.24382390.18334544X-RAY DIFFRACTION99
2.4168-2.46610.23162490.18034556X-RAY DIFFRACTION99
2.4661-2.51970.22682540.17824587X-RAY DIFFRACTION99
2.5197-2.57840.22872550.17984537X-RAY DIFFRACTION99
2.5784-2.64280.22532310.18034606X-RAY DIFFRACTION99
2.6428-2.71430.23742250.17934573X-RAY DIFFRACTION98
2.7143-2.79410.22982180.18854314X-RAY DIFFRACTION93
2.7941-2.88430.25252150.18994572X-RAY DIFFRACTION98
2.8843-2.98730.20672310.18654633X-RAY DIFFRACTION99
2.9873-3.10690.22492040.18374650X-RAY DIFFRACTION99
3.1069-3.24820.21292580.17994643X-RAY DIFFRACTION99
3.2482-3.41940.23582400.17954602X-RAY DIFFRACTION99
3.4194-3.63350.20422420.17344648X-RAY DIFFRACTION99
3.6335-3.91380.18872260.17094649X-RAY DIFFRACTION99
3.9138-4.30730.19532020.15484483X-RAY DIFFRACTION94
4.3073-4.92960.17422440.14534716X-RAY DIFFRACTION100
4.9296-6.2070.18982400.16614787X-RAY DIFFRACTION99
6.207-39.99770.16452460.15854793X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.20950.4344-0.3570.6477-0.5321.27890.0843-0.12890.12840.04810.0034-0.0015-0.41680.0501-0.11150.35840.0218-0.04730.24480.0410.270534.471410.4105-37.5259
22.59931.25-1.33581.7068-1.66983.24520.02750.23350.48190.14730.32030.5556-0.5676-0.7274-0.35550.38570.1333-0.03090.68520.06060.46678.70927.5354-24.6206
30.51610.09570.01710.6608-0.22191.32930.0789-0.130.06660.20580.0156-0.0682-0.4424-0.2038-0.07780.36760.00720.01880.3307-0.010.331623.23265.3658-7.483
41.27310.708-1.19981.8004-1.53673.8044-0.0949-0.2120.09260.14850.0521-0.1153-0.39740.52360.04970.38370.0216-0.04580.474-0.10810.386648.5868-1.71716.3963
51.16340.30470.90810.70640.01141.15850.0017-0.19040.1829-0.0547-0.04850.0679-0.3631-0.31460.05870.4680.06180.02050.35730.04640.367727.503713.4178-54.583
61.3263-0.2970.03491.0842-0.24261.40530.0501-0.0442-0.0965-0.0170.03540.1098-0.0878-0.175-0.08690.34080.00550.00760.25820.0680.295829.82351.2447-53.7085
70.5578-0.06870.25330.8403-0.54220.9472-0.00240.06620.0430.0435-0.0844-0.09650.0170.3040.08530.29360.01380.01850.32140.01890.240951.2889-15.3418-33.9506
80.61620.2931-0.22220.4004-0.18940.9164-0.0347-0.1050.02160.0235-0.02870.03890.05770.07410.06690.32070.04-0.0090.27970.02090.320135.5019-23.5982-25.3232
91.78610.3524-0.1691.3259-1.6765.59430.0141-0.2639-0.1579-0.0344-0.0483-0.00060.020.09680.0290.32450.02210.01850.20750.00470.322731.713-42.4895-12.5781
102.6284-1.8113-1.00654.2199-0.38262.3485-0.0424-0.2226-0.0705-0.0171-0.033-0.2778-0.06940.42840.08940.2515-0.0279-0.030.36020.06590.310455.5048-6.5868-36.0733
111.7031-0.7084-0.7891.66680.31162.17610.0446-0.1273-0.0591-0.0751-0.0333-0.1845-0.05280.3169-0.03340.2683-0.0229-0.01930.28720.0570.25146.5032-4.5356-39.008
120.6073-0.08271.45120.4349-0.2783.33510.1885-0.0845-0.01150.1951-0.0475-0.0947-0.1746-0.0933-0.13180.4074-0.0445-0.0320.47060.00560.323336.6688-0.993-7.7465
135.43873.7978-2.0476.92172.17178.28160.27040.0729-0.28050.935-0.3703-0.54940.42220.64070.09130.45410.0347-0.05770.58840.08060.452133.2322-10.124210.7383
149.7346-2.67011.4067.35732.83156.309-0.35850.1158-0.04560.6989-0.1663-0.8220.35022.17770.53170.51460.0736-0.03860.93490.08210.438837.023-10.92062.6971
150.407-0.09511.58830.2198-1.16765.92730.01690.01150.08920.08180.02160.0903-0.373-0.1134-0.03830.3580.04010.00610.35050.00480.319529.84635.0509-28.5759
164.11055.20022.2398.23170.68344.09290.22930.05682.8824-0.4728-1.0018-0.3775-2.35660.68760.5241.2036-0.00640.10750.51510.11251.45522.914433.1815-49.5823
174.3322-0.73141.19614.5171-2.05862.6824-0.04210.85191.2647-0.812-0.0050.2229-0.9942-0.4978-0.07310.9730.1534-0.03060.48570.14360.558522.522924.973-51.2196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 152 )
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 342 )
4X-RAY DIFFRACTION4chain 'A' and (resid 343 through 521 )
5X-RAY DIFFRACTION5chain 'A' and (resid 522 through 646 )
6X-RAY DIFFRACTION6chain 'A' and (resid 647 through 804 )
7X-RAY DIFFRACTION7chain 'A' and (resid 805 through 925 )
8X-RAY DIFFRACTION8chain 'A' and (resid 926 through 1112 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1113 through 1307 )
10X-RAY DIFFRACTION10chain 'B' and (resid -19 through -10 )
11X-RAY DIFFRACTION11chain 'B' and (resid -9 through 5 )
12X-RAY DIFFRACTION12chain 'B' and (resid 6 through 15 )
13X-RAY DIFFRACTION13chain 'B' and (resid 16 through 20 )
14X-RAY DIFFRACTION14chain 'C' and (resid -19 through -15 )
15X-RAY DIFFRACTION15chain 'C' and (resid -14 through 5 )
16X-RAY DIFFRACTION16chain 'C' and (resid 6 through 10 )
17X-RAY DIFFRACTION17chain 'D' and (resid -10 through -1 )

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