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- PDB-5ecj: Crystal structure of monobody Mb(S4) bound to Prdm14 in complex w... -

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Basic information

Entry
Database: PDB / ID: 5ecj
TitleCrystal structure of monobody Mb(S4) bound to Prdm14 in complex with Mtgr1
Components
  • Monobody Mb(S4)
  • PR domain zinc finger protein 14,Protein CBFA2T2
KeywordsGENE REGULATION/TRANSCRIPTION / TRANSFERASE / PROTEIN BINDING / GENE REGULATION-TRANSCRIPTION complex
Function / homology
Function and homology information


: / : / inner cell mass cell fate commitment / positive regulation of flagellated sperm motility / intestinal epithelial cell differentiation / negative regulation of fibroblast growth factor receptor signaling pathway / germ-line stem cell population maintenance / fertilization / : / cell fate specification ...: / : / inner cell mass cell fate commitment / positive regulation of flagellated sperm motility / intestinal epithelial cell differentiation / negative regulation of fibroblast growth factor receptor signaling pathway / germ-line stem cell population maintenance / fertilization / : / cell fate specification / stem cell population maintenance / positive regulation of stem cell population maintenance / negative regulation of Notch signaling pathway / germ cell development / epigenetic regulation of gene expression / homeostasis of number of cells within a tissue / embryo implantation / epithelial cell differentiation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cell morphogenesis / chromatin DNA binding / positive regulation of neuron projection development / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / negative regulation of neuron projection development / regulation of gene expression / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Myeloid transforming gene-related protein-1 (MTGR1) / PRDM14, PR/SET domain / CBFA2T family / NHR2-like / NHR2 domain like / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 ...Myeloid transforming gene-related protein-1 (MTGR1) / PRDM14, PR/SET domain / CBFA2T family / NHR2-like / NHR2 domain like / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / Zinc finger, C2H2 type / SET domain profile. / SET domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PR domain zinc finger protein 14 / Protein CBFA2T2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.05 Å
AuthorsGupta, A. / Koide, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA036887 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM090324 United States
CitationJournal: Elife / Year: 2015
Title: ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation.
Authors: Nady, N. / Gupta, A. / Ma, Z. / Swigut, T. / Koide, A. / Koide, S. / Wysocka, J.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR domain zinc finger protein 14,Protein CBFA2T2
F: Monobody Mb(S4)
B: PR domain zinc finger protein 14,Protein CBFA2T2
E: Monobody Mb(S4)


Theoretical massNumber of molelcules
Total (without water)89,4434
Polymers89,4434
Non-polymers00
Water0
1
A: PR domain zinc finger protein 14,Protein CBFA2T2
E: Monobody Mb(S4)


Theoretical massNumber of molelcules
Total (without water)44,7222
Polymers44,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Monobody Mb(S4)
B: PR domain zinc finger protein 14,Protein CBFA2T2


Theoretical massNumber of molelcules
Total (without water)44,7222
Polymers44,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.812, 106.812, 180.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PR domain zinc finger protein 14,Protein CBFA2T2 / PR domain-containing protein 14 / MTG8-like protein / MTG8-related protein 1


Mass: 34523.152 Da / Num. of mol.: 2 / Mutation: L200H,L200H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prdm14, Cbfa2t2, Cbfa2t2h, Mtgr1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E9Q3T6, UniProt: O70374, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Monobody Mb(S4)


Mass: 10198.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 17% PEG3350, 8% Tacsimate / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.05→37.764 Å / Num. obs: 20631 / % possible obs: 99.9 % / Redundancy: 20 % / Net I/σ(I): 30
Reflection shellResolution: 3.05→3.16 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 3.05→37.764 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 1725 8.38 %
Rwork0.1886 --
obs0.1939 20581 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→37.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 0 0 5480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065617
X-RAY DIFFRACTIONf_angle_d1.0747648
X-RAY DIFFRACTIONf_dihedral_angle_d13.6651972
X-RAY DIFFRACTIONf_chiral_restr0.042856
X-RAY DIFFRACTIONf_plane_restr0.006991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.13970.34691420.28341547X-RAY DIFFRACTION100
3.1397-3.2410.38321400.28661529X-RAY DIFFRACTION100
3.241-3.35680.41561390.26611536X-RAY DIFFRACTION100
3.3568-3.49110.31421410.24941536X-RAY DIFFRACTION100
3.4911-3.64990.33651410.22191544X-RAY DIFFRACTION100
3.6499-3.84210.28061430.20091574X-RAY DIFFRACTION100
3.8421-4.08260.23171410.18511550X-RAY DIFFRACTION100
4.0826-4.39740.25751430.15551561X-RAY DIFFRACTION100
4.3974-4.83910.20321450.14871583X-RAY DIFFRACTION100
4.8391-5.53740.2141450.15751588X-RAY DIFFRACTION100
5.5374-6.96940.25531480.20151621X-RAY DIFFRACTION100
6.9694-37.76660.21851570.18381687X-RAY DIFFRACTION98
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)
15.6097-1.7366-0.45123.58894.24045.7687-0.27490.2276-1.34233.2876-0.46211.61190.8622-0.36270.56362.13240.144-0.14460.60930.11.1654-2.365825.57035.6303
24.217-0.5140.85755.33520.02835.8059-0.00620.2243-0.17750.8862-0.1323-1.0184-0.07581.29830.23280.91390.0012-0.26150.9215-0.00981.01225.932243.6038-1.8187
36.1326-0.1585-1.72996.2130.47182.9354-0.07160.3324-0.33240.02040.33490.1259-0.4251-0.0509-0.29380.8253-0.0215-0.22560.7441-0.04060.5964-3.924839.7721-7.7071
45.55141.69880.43056.2303-0.4033.3429-0.17330.5099-1.5569-0.04330.231-0.50040.81970.3241-0.21.07490.3073-0.20230.907-0.40631.247-2.139720.5093-11.628
52.51440.17210.83645.03983.16644.58620.6555-0.4146-0.4058-1.44020.82630.43340.3524-0.21150.97481.8536-0.3854-0.87121.4956-0.20221.0152-25.537413.445426.1752
63.15892.27811.08942.2721-0.44423.9015-0.0276-0.8152-0.09512.0783-0.376-0.48170.3080.76440.5551.5185-0.26820.0211.29610.23230.8693-29.25461.882519.9773
78.4895-1.1073-3.26182.05840.67372.05520.4279-0.2589-0.2975-0.2726-0.4582-1.4421-1.2060.622-0.07341.011-0.09970.00111.18750.12381.256-25.84668.463610.7317
86.19421.08151.14082.0618-0.02268.81290.5917-1.459-0.28820.2377-0.443-0.8267-1.81340.0649-0.12131.0147-0.3399-0.01421.46970.11660.778-27.03275.683714.5363
96.45070.22430.91325.3035-0.80089.08160.8204-1.3868-0.73670.7163-0.98310.4233-2.1607-0.28910.31240.7512-0.4823-0.35991.51320.00840.8743-23.703311.393518.042
105.5712-4.5376.17327.1373-3.89777.3113-0.46310.4330.44173.10280.1340.9182-1.53631.00440.37891.64260.0334-0.24480.669-0.03931.6052-31.871644.7052-14.2214
112.82574.3946-2.87286.8085-5.24934.47040.0132-1.8061.67580.1494-0.81530.8054-0.63710.84621.22321.51370.3104-0.2171.3355-0.40871.2284-40.018439.49633.0356
122.7646-3.05612.18574.4562-1.22992.7242-0.2959-1.41262.115-0.2481-0.34140.0626-0.167-2.27360.86081.85460.39980.02851.4354-0.47261.3971-43.16135.94995.7651
137.87121.35131.63295.6818-0.74196.91330.2629-0.90640.08911.0455-0.10320.1954-0.3031-0.7547-0.18431.1160.10360.02310.8076-0.2250.7613-39.16722.1505-2.0152
144.5428-1.0728-2.07941.3302-0.18562.4820.0716-0.69130.1341.7243-0.0557-0.5908-0.72010.47790.00491.2787-0.1799-0.17110.6691-0.2580.8583-30.4324.31280.6899
154.3092-1.88010.7046.3357-2.10336.2051-0.28670.132-0.6462-0.76250.69230.53831.1151-0.0785-0.40110.9671-0.1157-0.21310.6626-0.06070.8448-32.173315.2454-10.3667
162.9652-0.54071.66184.7971-3.4475.2653-0.15620.84360.59990.33110.0494-0.63970.23750.9430.14920.86560.0329-0.18780.8528-0.21180.9671-24.221834.211-20.1984
174.3815-0.7061-0.89994.64476.44058.3628-0.5550.77-0.3712-0.39330.13142.01360.15-0.51060.17010.92990.2533-0.17861.0112-0.05881.0233-37.72134.6712-18.0263
182.461-1.2159-0.28122.28453.34726.0284-0.3696-0.48560.03690.4082-0.20682.7588-1.5278-0.31610.44981.11720.31740.06940.9281-0.22721.2121-15.523769.37840.6217
192.02071.1951-1.31782.6196-2.66232.71150.2410.8336-0.2054-1.10550.18161.84420.13110.19110.56220.842-0.0468-0.1390.92950.14160.7434-11.533173.8233-18.0498
209.2886-2.2621-2.82288.7167-2.91062.4738-0.19871.05210.1547-1.17960.22920.46620.749-0.15280.04140.9757-0.2034-0.32080.6030.03890.674-9.556770.3406-18.5881
218.67694.79586.69486.17695.87116.5738-0.6064-0.50471.05551.2428-0.05190.4369-0.51490.4918-0.01541.30970.1984-0.03450.68840.01320.6066-9.871865.0216-4.4378
223.7432-0.40755.22441.6552-0.31357.3120.32062.2022-1.40780.3691-0.22441.01420.376-0.65470.09860.7491-0.045-0.38031.5039-0.22371.1782-19.854755.6292-18.6959
235.5697-2.4045-0.67572.5725-1.532.658-0.2361-0.7395-0.3217-1.5966-0.3127-1.17691.40670.55970.78121.35190.2877-0.35971.01520.03350.9026-6.484760.3471-9.7029
243.34931.5659-0.62778.26961.46354.40950.91060.8863-0.01880.8021-0.1445-0.4266-0.53210.2010.4391.3063-0.0632-0.35840.54480.12261.0282-8.624766.7594-16.2074
253.74071.0479-2.06075.27420.27343.0377-0.32220.49110.36391.66260.06070.38661.53620.17330.05220.82580.0738-0.11470.58980.13340.7157-13.242562.1492-5.8095
265.12322.6736-1.7047.39562.82043.0547-0.6969-2.41680.25882.408-0.26640.2211-0.05180.2171-0.09461.66950.1846-0.04630.7701-0.14470.7351-11.812558.47955.9786
276.0041-2.4918-0.25127.53132.03240.5880.7417-1.2065-0.22251.86970.07540.05620.4666-0.3781-0.27390.58160.1238-0.23810.27580.50211.3851-18.88369.0336-16.195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 225 )
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 288 )
5X-RAY DIFFRACTION5chain 'F' and (resid 1 through 8 )
6X-RAY DIFFRACTION6chain 'F' and (resid 9 through 28 )
7X-RAY DIFFRACTION7chain 'F' and (resid 29 through 51 )
8X-RAY DIFFRACTION8chain 'F' and (resid 52 through 77 )
9X-RAY DIFFRACTION9chain 'F' and (resid 78 through 93 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 14 )
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 53 )
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 150 )
14X-RAY DIFFRACTION14chain 'B' and (resid 151 through 181 )
15X-RAY DIFFRACTION15chain 'B' and (resid 182 through 206 )
16X-RAY DIFFRACTION16chain 'B' and (resid 207 through 263 )
17X-RAY DIFFRACTION17chain 'B' and (resid 264 through 286 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 8 )
19X-RAY DIFFRACTION19chain 'E' and (resid 9 through 14 )
20X-RAY DIFFRACTION20chain 'E' and (resid 15 through 21 )
21X-RAY DIFFRACTION21chain 'E' and (resid 22 through 38 )
22X-RAY DIFFRACTION22chain 'E' and (resid 39 through 45 )
23X-RAY DIFFRACTION23chain 'E' and (resid 46 through 51 )
24X-RAY DIFFRACTION24chain 'E' and (resid 52 through 66 )
25X-RAY DIFFRACTION25chain 'E' and (resid 67 through 77 )
26X-RAY DIFFRACTION26chain 'E' and (resid 78 through 86 )
27X-RAY DIFFRACTION27chain 'E' and (resid 87 through 93 )

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