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- PDB-3wst: Crystal structure of C.elegans PRMT7 in complex with SAH(P31) -

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Basic information

Entry
Database: PDB / ID: 3wst
TitleCrystal structure of C.elegans PRMT7 in complex with SAH(P31)
ComponentsProtein arginine N-methyltransferase 7
KeywordsTRANSFERASE / Rossmann fold
Function / homology
Function and homology information


RMTs methylate histone arginines / protein-arginine omega-N monomethyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
Protein arginine N-methyltransferase PRMT7 / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Protein arginine N-methyltransferase PRMT7 / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 7
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsHasegawa, M. / Toma-fukai, S. / Shimizu, T.
CitationJournal: Febs Lett. / Year: 2014
Title: Protein arginine methyltransferase 7 has a novel homodimer-like structure formed by tandem repeats
Authors: Hasegawa, M. / Toma-fukai, S. / Kim, J.D. / Fukamizu, A. / Shimizu, T.
History
DepositionMar 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 7
D: Protein arginine N-methyltransferase 7
B: Protein arginine N-methyltransferase 7
C: Protein arginine N-methyltransferase 7
F: Protein arginine N-methyltransferase 7
E: Protein arginine N-methyltransferase 7
G: Protein arginine N-methyltransferase 7
H: Protein arginine N-methyltransferase 7
I: Protein arginine N-methyltransferase 7
M: Protein arginine N-methyltransferase 7
N: Protein arginine N-methyltransferase 7
O: Protein arginine N-methyltransferase 7
P: Protein arginine N-methyltransferase 7
Q: Protein arginine N-methyltransferase 7
R: Protein arginine N-methyltransferase 7
J: Protein arginine N-methyltransferase 7
K: Protein arginine N-methyltransferase 7
L: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,342,33854
Polymers1,333,70918
Non-polymers8,62936
Water9,206511
1
A: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
M: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
N: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
O: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
P: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
Q: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
R: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
J: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
17
K: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
18
L: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,0951
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)190.703, 190.703, 373.088
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Protein arginine N-methyltransferase 7


Mass: 74094.930 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pmrt-2, prmt-7, W06D4.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9XW42, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2M ammonium phosphate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 593769 / Redundancy: 5.8 % / Rsym value: 0.123 / Net I/σ(I): 21.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→47.41 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.883 / SU B: 11.84 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30328 29764 5 %RANDOM
Rwork0.23354 ---
obs0.23702 563621 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.338 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.39→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms91576 0 558 511 92645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0294147
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.952127160
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.644511456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1324.5164497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.5481516623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.35315504
X-RAY DIFFRACTIONr_chiral_restr0.1290.213823
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02171012
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.453 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 2124 -
Rwork0.367 40055 -
obs--95.17 %

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