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- PDB-7dc3: Crystal structure of the MyRF ICA domain -

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Basic information

Entry
Database: PDB / ID: 7dc3
TitleCrystal structure of the MyRF ICA domain
ComponentsIsoform 2 of Myelin regulatory factor
KeywordsMEMBRANE PROTEIN / auto-catalytic protease / protein chaperone. trimeric protein / triple coiled-coil
Function / homology
Function and homology information


central nervous system myelin maintenance / central nervous system myelination / positive regulation of myelination / oligodendrocyte development / Hydrolases; Acting on peptide bonds (peptidases) / oligodendrocyte differentiation / protein autoprocessing / peptidase activity / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...central nervous system myelin maintenance / central nervous system myelination / positive regulation of myelination / oligodendrocyte development / Hydrolases; Acting on peptide bonds (peptidases) / oligodendrocyte differentiation / protein autoprocessing / peptidase activity / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Myelin gene regulatory factor C-terminal domain 2 / Myelin gene regulatory factor, ICA domain / Myelin regulatory factor ICA domain / Myelin gene regulatory factor C-terminal domain 2 / NDT80 DNA-binding domain / NDT80 DNA-binding domain superfamily / NDT80 / PhoG like DNA-binding family / NDT80 DNA-binding domain profile. / Chaperone of endosialidase / Intramolecular chaperone auto-processing domain ...Myelin gene regulatory factor C-terminal domain 2 / Myelin gene regulatory factor, ICA domain / Myelin regulatory factor ICA domain / Myelin gene regulatory factor C-terminal domain 2 / NDT80 DNA-binding domain / NDT80 DNA-binding domain superfamily / NDT80 / PhoG like DNA-binding family / NDT80 DNA-binding domain profile. / Chaperone of endosialidase / Intramolecular chaperone auto-processing domain / Intramolecular chaperone auto-processing (ICA) domain profile. / p53-like transcription factor, DNA-binding
Similarity search - Domain/homology
Myelin regulatory factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsShi, N. / Wu, P. / Zhen, X.K. / Li, B.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)Grants 31570763 China
Chinese Academy of SciencesHundreds Talents Program China
CitationJournal: Int J Biol Sci / Year: 2021
Title: Crystal structure of the MyRF ICA domain with its upstream beta-helical stalk reveals the molecular mechanisms underlying its trimerization and self-cleavage.
Authors: Wu, P. / Zhen, X. / Li, B. / Yu, Q. / Huang, X. / Shi, N.
History
DepositionOct 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Myelin regulatory factor
B: Isoform 2 of Myelin regulatory factor
C: Isoform 2 of Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)61,4543
Polymers61,4543
Non-polymers00
Water1,53185
1
A: Isoform 2 of Myelin regulatory factor

A: Isoform 2 of Myelin regulatory factor

A: Isoform 2 of Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)61,4543
Polymers61,4543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
2
B: Isoform 2 of Myelin regulatory factor

B: Isoform 2 of Myelin regulatory factor

B: Isoform 2 of Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)61,4543
Polymers61,4543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
3
C: Isoform 2 of Myelin regulatory factor

C: Isoform 2 of Myelin regulatory factor

C: Isoform 2 of Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)61,4543
Polymers61,4543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)78.706, 78.706, 138.464
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-801-

HOH

21B-854-

HOH

31C-802-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 568 through 705)
d_2ens_1chain "B"
d_3ens_1(chain "C" and resid 568 through 705)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPLYSA10 - 147
d_21ens_1ASPLYSB1 - 138
d_31ens_1ASPLYSC5 - 142

NCS oper:
IDCodeMatrixVector
1given(0.492176376521, -0.870493311347, 0.00195174146644), (-0.870488685258, -0.492180158132, -0.00285320487778), (0.00344430418559, -0.000294688824867, -0.999994024946)39.390721841, 67.956633254, 47.7375249749
2given(0.863283285217, 0.504715934663, 0.00194801524934), (0.504719302412, -0.863280993071, -0.00208633072194), (0.000628680178621, 0.00278429533742, -0.999995926222)-23.1174531754, 39.361757157, 92.9795132673

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Components

#1: Protein Isoform 2 of Myelin regulatory factor / Myelin gene regulatory factor


Mass: 20484.744 Da / Num. of mol.: 3 / Mutation: S587A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myrf, Gm1804, Gm98, Mrf / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q3UR85, Hydrolases; Acting on peptide bonds (peptidases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, Lithium chloride, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→38.22 Å / Num. obs: 20050 / % possible obs: 96 % / Redundancy: 18.2 % / Biso Wilson estimate: 30.67 Å2 / CC1/2: 0.971 / CC star: 0.993 / Net I/σ(I): 16.78
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 13.2 % / Num. unique obs: 1965 / CC1/2: 0.0291 / CC star: 0.238 / % possible all: 69.9

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
PHENIX1.19rc3_4028refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→38.22 Å / SU ML: 0.3493 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 3123 8.84 %
Rwork0.217 32192 -
obs-19263 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 0 85 3468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243433
X-RAY DIFFRACTIONf_angle_d0.47014633
X-RAY DIFFRACTIONf_chiral_restr0.0429535
X-RAY DIFFRACTIONf_plane_restr0.0056603
X-RAY DIFFRACTIONf_dihedral_angle_d11.87211311
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.878485516038
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.871001277512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.3343810.306931X-RAY DIFFRACTION59.67
2.44-2.480.34541000.301975X-RAY DIFFRACTION62.9
2.48-2.520.33241030.31481158X-RAY DIFFRACTION74.31
2.52-2.570.36531420.32491325X-RAY DIFFRACTION85.19
2.57-2.620.34381440.29631436X-RAY DIFFRACTION92.02
2.62-2.670.30961430.29291479X-RAY DIFFRACTION97.95
2.67-2.730.33431550.30341561X-RAY DIFFRACTION98.28
2.73-2.790.31381480.29691559X-RAY DIFFRACTION99.88
2.79-2.860.35571380.29021523X-RAY DIFFRACTION99.7
2.86-2.940.27771580.23821597X-RAY DIFFRACTION100
2.94-3.020.31861520.23711540X-RAY DIFFRACTION99.94
3.02-3.120.28281500.23261560X-RAY DIFFRACTION100
3.12-3.230.30611410.2131533X-RAY DIFFRACTION100
3.23-3.360.29291580.21251560X-RAY DIFFRACTION100
3.36-3.510.2211560.19291531X-RAY DIFFRACTION100
3.52-3.70.21231580.17371561X-RAY DIFFRACTION100
3.7-3.930.21631540.18011571X-RAY DIFFRACTION100
3.93-4.240.2371520.18711546X-RAY DIFFRACTION100
4.24-4.660.17761520.15051565X-RAY DIFFRACTION100
4.66-5.330.24191460.17351547X-RAY DIFFRACTION99.47
5.33-6.710.27091430.21731567X-RAY DIFFRACTION99.94
6.71-38.220.2571490.1931567X-RAY DIFFRACTION99.77
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)
10.885710333337-0.2638107234050.1498805168760.847802593687-0.2741016034694.38118928128-0.0878981785729-0.372482341136-0.21358158890.4469024247040.0436349637856-0.02341182921470.8525443021850.2596461474610.08455171388610.436855605020.03280885960120.02596499849890.3202452892030.06874416270630.1862820834921.6974856236938.57187211441.744295545
20.652625502529-0.09440477872260.5913658196481.551487419090.4344565607384.81605980255-0.122047261603-0.221996025806-0.1092956300520.325904658996-0.0531914907207-0.4291510658040.526920841670.9646774275880.0274482803280.3539699602690.0461865969845-0.06480459153720.4924794451820.08128424779690.230179207077.9396800970240.6247968851.4806754049
30.393877318128-0.6601456096210.08144034102581.963166561650.05951698199712.731495714010.1186903772840.04453340301110.202332988593-0.225200902466-0.00816545140885-0.304550042936-0.3310059950940.3126540265420.02182377420520.233231489151-0.01707500368740.03214272387520.0710245512499-0.007698911027810.170102613864.0965673226952.72469553979.02622733053
42.25895906502-0.206638604932.700177606141.870477152-0.1476800919678.80211219587-0.2723312185880.4565275519580.115468085756-0.3324200344460.1116375528120.00102545552565-1.01619123359-0.1255681467250.1953529083950.223433184566-0.02572568913550.05232540157140.2679322985130.009188896589840.1862333171171.4645520506850.4836229122-21.0372350478
52.46346887871-1.599918581260.658925106413.29862153246-2.095463119037.025050460980.06920517784980.410621820155-0.0636644063656-0.444775742156-0.2565247591760.227092850881-0.700620417012-0.7643308147430.2179763844220.4508563740830.127108629395-0.03860610211780.424302654488-0.1142640711550.797408582722-6.514430563134.9017198427855.9604865116
62.251227043250.2703656661460.3412296162190.874137319830.6149033705747.27891644273-0.2457773352790.4815844680580.161486090046-0.4505379550320.0177009350171-0.260983642599-1.439658231360.8519787752140.2142952847320.69878690099-0.0985963689323-0.01430644032580.4723466681980.1650930220530.8269352521524.283847959898.5565846733340.9294122608
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 559 through 615 )AA559 - 6151 - 57
22chain 'A' and (resid 616 through 705 )AA616 - 70558 - 147
33chain 'B' and (resid 568 through 599 )BB568 - 5991 - 32
44chain 'B' and (resid 671 through 705 )BB671 - 705104 - 138
55chain 'C' and (resid 564 through 599 )CC564 - 5991 - 36
66chain 'C' and (resid 600 through 705 )CC600 - 70537 - 142

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