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- PDB-9l12: Crystal structure of Cas12h ternary complex -

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Basic information

Entry
Database: PDB / ID: 9l12
TitleCrystal structure of Cas12h ternary complex
Components
  • Cas12h
  • DNA (28-MER)
  • DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')
  • RNA (56-MER)
KeywordsDNA BINDING PROTEIN / RNA / DNA / Complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified (others)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å
AuthorsXiang, W. / Chen, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Rep / Year: 2025
Title: Cas12h is a crRNA-guided DNA nickase that can be utilized for precise gene editing.
Authors: Xiang, W. / Lin, X. / Yang, Y. / Huang, L. / Chen, Y. / Chen, J. / Liu, L.
History
DepositionDec 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cas12h
B: DNA (28-MER)
C: DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')
D: RNA (56-MER)
E: Cas12h
F: DNA (28-MER)
G: DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')
H: RNA (56-MER)
I: Cas12h
J: DNA (28-MER)
K: DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')
L: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,03315
Polymers393,96012
Non-polymers733
Water00
1
A: Cas12h
B: DNA (28-MER)
C: DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')
D: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3445
Polymers131,3204
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16450 Å2
ΔGint-104 kcal/mol
Surface area55750 Å2
MethodPISA
2
E: Cas12h
F: DNA (28-MER)
G: DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')
H: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3445
Polymers131,3204
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17120 Å2
ΔGint-107 kcal/mol
Surface area57440 Å2
MethodPISA
3
I: Cas12h
J: DNA (28-MER)
K: DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')
L: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3445
Polymers131,3204
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16470 Å2
ΔGint-104 kcal/mol
Surface area56120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.527, 155.527, 479.655
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
14
24
34

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASPASP(chain 'A' and (resid 1 through 124 or (resid 125...AA1 - 6651 - 665
121ARGARGLYSLYS(chain 'A' and (resid 1 through 124 or (resid 125...AA669 - 764669 - 764
131GLYGLYVALVAL(chain 'A' and (resid 1 through 124 or (resid 125...AA776 - 870776 - 870
211METMETASPASP(chain 'E' and (resid 1 through 665 or resid 669 through 765 or resid 776 through 870))EE1 - 6651 - 665
221ARGARGLYSLYS(chain 'E' and (resid 1 through 665 or resid 669 through 765 or resid 776 through 870))EE669 - 764669 - 764
231GLYGLYVALVAL(chain 'E' and (resid 1 through 665 or resid 669 through 765 or resid 776 through 870))EE776 - 870776 - 870
311METMETASPASP(chain 'I' and (resid 1 through 124 or (resid 125...II1 - 6651 - 665
321ARGARGLYSLYS(chain 'I' and (resid 1 through 124 or (resid 125...II669 - 764669 - 764
331GLYGLYVALVAL(chain 'I' and (resid 1 through 124 or (resid 125...II776 - 870776 - 870
112DADADTDTchain 'B'BB1 - 281 - 28
212DADADTDTchain 'F'FF1 - 281 - 28
312DADADTDTchain 'J'JJ1 - 281 - 28
113DADADCDC(chain 'C' and resid 1 through 11)CC1 - 111 - 11
213DADADCDCchain 'K'KK1 - 111 - 11
114GGCCchain 'D'DD0 - 551 - 56
214GGCCchain 'H'HH0 - 551 - 56
314GGCCchain 'L'LL0 - 551 - 56

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Cas12h


Mass: 100025.758 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: DNA chain DNA (28-MER)


Mass: 8603.523 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*GP*TP*CP*GP*AP*TP*GP*TP*TP*CP*T)-3')


Mass: 4565.968 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain RNA (56-MER)


Mass: 18124.877 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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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: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Tris-HCl, 0.2 M Magnesium chloride, 31% PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979852 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 79206 / % possible obs: 94.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 21.98 Å2 / Rpim(I) all: 0.115 / Net I/σ(I): 4
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 4.2 % / Num. unique obs: 3586 / Rpim(I) all: 0.449 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHENIX1.17.1_3660phasing
Coot0.7.2.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 3.81→28.42 Å / SU ML: 0.8141 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.8047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3392 2905 3.67 %
Rwork0.3343 76301 -
obs0.3345 79206 62.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.5 Å2
Refinement stepCycle: LAST / Resolution: 3.81→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20879 6114 3 0 26996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004928151
X-RAY DIFFRACTIONf_angle_d1.190539331
X-RAY DIFFRACTIONf_chiral_restr0.06794410
X-RAY DIFFRACTIONf_plane_restr0.00573995
X-RAY DIFFRACTIONf_dihedral_angle_d24.246811347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.81-3.870.779620.362542X-RAY DIFFRACTION0.73
3.87-3.940.4237170.4042491X-RAY DIFFRACTION8.57
3.94-4.010.4366560.39381439X-RAY DIFFRACTION24.61
4.01-4.080.4051770.37942094X-RAY DIFFRACTION35.69
4.08-4.170.4114910.39752331X-RAY DIFFRACTION40.49
4.17-4.260.403990.36672603X-RAY DIFFRACTION45.03
4.26-4.360.3716990.38122736X-RAY DIFFRACTION46.64
4.36-4.460.32941100.37662764X-RAY DIFFRACTION47.5
4.46-4.580.34881080.37822896X-RAY DIFFRACTION49.51
4.59-4.720.36711130.37573049X-RAY DIFFRACTION52.26
4.72-4.870.31921490.37083752X-RAY DIFFRACTION65.19
4.87-5.040.39651600.35234518X-RAY DIFFRACTION77.25
5.04-5.240.4161930.3644862X-RAY DIFFRACTION83.72
5.24-5.480.38721990.36774965X-RAY DIFFRACTION85.61
5.48-5.770.35681950.36925162X-RAY DIFFRACTION87.98
5.77-6.130.38191960.36385124X-RAY DIFFRACTION88.92
6.13-6.590.36271970.34975236X-RAY DIFFRACTION89.94
6.59-7.250.38772060.34075341X-RAY DIFFRACTION92.17
7.25-8.270.31292080.30595537X-RAY DIFFRACTION94.38
8.27-10.340.25032110.25885667X-RAY DIFFRACTION97.14
10.34-28.420.22122190.23195692X-RAY DIFFRACTION98.14

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