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- PDB-2v7e: Crystal structure of coactivator-associated arginine methyltransf... -

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Basic information

Entry
Database: PDB / ID: 2v7e
TitleCrystal structure of coactivator-associated arginine methyltransferase 1 (CARM1), unliganded
ComponentsHISTONE-ARGININE METHYLTRANSFERASE CARM1
KeywordsTRANSFERASE / ARGININE METHYLTRANSFERASE / S-ADENOSYL-L-METHIONINE / TRANSCRIPTION REGULATION / HISTONE MODIFICATION / CO- ACTIVATOR / METHYLTRANSFERASE / CHROMATIN REGULATOR / NUCLEUS / TRANSCRIPTION
Function / homology
Function and homology information


regulation of growth plate cartilage chondrocyte proliferation / histone H3R26 methyltransferase activity / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase ...regulation of growth plate cartilage chondrocyte proliferation / histone H3R26 methyltransferase activity / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / Estrogen-dependent gene expression / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / histone methyltransferase activity / nuclear replication fork / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of fat cell differentiation / estrogen receptor signaling pathway / protein localization to chromatin / RNA polymerase II transcription regulator complex / methylation / transcription coactivator activity / cell population proliferation / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytosol
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYue, W.W. / Hassler, M. / Roe, S.M. / Thompson-Vale, V. / Pearl, L.H.
CitationJournal: Embo J. / Year: 2007
Title: Insights Into Histone Code Syntax from Structural and Biochemical Studies of Carm1 Methyltransferase
Authors: Yue, W.W. / Hassler, M. / Roe, S.M. / Thompson-Vale, V. / Pearl, L.H.
History
DepositionJul 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE-ARGININE METHYLTRANSFERASE CARM1
B: HISTONE-ARGININE METHYLTRANSFERASE CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8115
Polymers78,2092
Non-polymers6023
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-37.4 kcal/mol
Surface area32000 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.146, 98.018, 206.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

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Components

#1: Protein HISTONE-ARGININE METHYLTRANSFERASE CARM1 / PROTEIN ARGININE N-METHYLTRANSFERASE 4 / COACTIVATOR-ASSOCIATED ARGININE METHYLTRANSFERASE 1


Mass: 39104.582 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 147-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC-HTA / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9WVG6, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 145 AND 146 OF CHAINS A AND B ARE VECTOR-DERIVED SEQUENCE (VECTOR USED IS PFASTBAC-HTA).

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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: 2.41 Å3/Da / Density % sol: 48.99 % / Description: NONE
Crystal growpH: 7.5
Details: 1.6M DI-AMMONIUM HYDROGENPHOSPHATE, 100MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9776
DetectorDetector: CCD / Date: Dec 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 19941 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ORI

1ori


Resolution: 2.7→30.69 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 30.831 / SU ML: 0.31 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. CRYOBUFFER CONTAINS 1MM EMP. 3 PARTIALLY- DISORDERED HG ATOMS WITH LOW OCCUPANCY (< 0.5) WERE FOUND CLOSE TO CYS194 CHAIN B, CYS439 CHAIN A AND CYS421 CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1082 5.2 %RANDOM
Rwork0.228 ---
obs0.23 19925 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20 Å2
2--0.09 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 3 104 5146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225169
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9427025
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84824.224232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01115829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3341520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023931
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22351
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23498
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2241.53294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.39725159
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.58632138
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9094.51866
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: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 74
Rwork0.274 1437
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
118.873-2.36890.26142.83940.15562.77460.43130.40180.3214-0.2707-0.20330.0774-0.07120.039-0.228-0.0294-0.06970.0221-0.22640.0355-0.277716.91-38.67735.543
26.94182.2216-6.54978.57623.02279.51120.31410.23690.2197-0.6393-0.21260.2338-0.7891-0.2223-0.10150.0383-0.0724-0.0279-0.26850.012-0.247820.304-33.27245.502
32.80251.5763-1.3772.1653-0.3813.15230.07880.19120.2536-0.0410.1196-0.0506-0.94630.0514-0.19840.1342-0.03270.0469-0.115-0.0434-0.190618.696-27.59742.194
40.8383-0.5906-0.00460.5398-0.24990.51770.15460.39780.263-0.0621-0.2483-0.0816-0.17560.08220.09370.2422-0.05070.1004-0.03020.0185-0.14847.948-21.48415.028
52.7518-0.38631.90811.1518-2.37315.36110.07320.14150.13930.0050.0462-0.0192-0.36570.2922-0.11940.134-0.02260.096-0.0859-0.0475-0.214320.214-28.32816.124
61.57911.12641.05942.5828-0.36657.2610.0059-0.44550.34470.41950.03040.8235-1.4891-0.4082-0.03630.40680.12210.16020.2260.04910.086616.01-18.27412.455
78.3515-2.4521-1.57666.0983-0.07284.78870.27290.2089-0.118-0.2521-0.08840.1289-0.2789-0.3848-0.18450.18340.10260.0662-0.17130.0228-0.3473-20.014-15.4415.311
83.48371.5322-3.22723.66480.82078.28470.3615-0.13760.32740.1002-0.024-0.2671-0.86810.2766-0.33750.53430.08830.0921-0.13280.0348-0.1282-16.318-2.40717.932
91.1132-0.15670.42740.2469-0.1810.75560.0807-0.0048-0.02030.0532-0.02190.0944-0.2236-0.175-0.0588-0.01740.04260.062-0.22580.0029-0.3191-13.185-26.70134.624
102.0951-1.2275-0.50264.0939-0.60713.3011-0.00740.0592-0.1215-0.05110.02730.28640.0731-0.4817-0.0198-0.17460.01720.0188-0.1654-0.0303-0.2764-24.382-28.35831.749
114.66881.5649-1.4934.47090.55113.8048-0.0881-0.243-0.00060.02590.02250.13140.1769-0.10380.0656-0.03170.07490.0076-0.16480.0086-0.2922-19.318-31.95443.18
1212.99876.0453-7.5455.6882-2.79688.90570.1642-0.8077-0.49520.6959-0.5-0.079-0.08810.21710.3358-0.04810.1280.0246-0.17190.0059-0.2089-16.2-34.91241.794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A155 - 184
2X-RAY DIFFRACTION2A185 - 221
3X-RAY DIFFRACTION3A222 - 275
4X-RAY DIFFRACTION4A276 - 335
5X-RAY DIFFRACTION5A336 - 429
6X-RAY DIFFRACTION6A430 - 476
7X-RAY DIFFRACTION7B155 - 185
8X-RAY DIFFRACTION8B186 - 250
9X-RAY DIFFRACTION9B251 - 336
10X-RAY DIFFRACTION10B337 - 422
11X-RAY DIFFRACTION11B423 - 455
12X-RAY DIFFRACTION12B456 - 476

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