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- PDB-5wc9: Human Pit-1 and 4xCATT DNA complex -

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Basic information

Entry
Database: PDB / ID: 5wc9
TitleHuman Pit-1 and 4xCATT DNA complex
Components
  • DNA (5'-D(*CP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*GP*GP*A)-3')
  • DNA (5'-D(*CP*CP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*GP*T)-3')
  • Pituitary-specific positive transcription factor 1
KeywordsDNA BINDING PROTEIN / Transcription regulation / DNA-protein Complex
Function / homology
Function and homology information


adenohypophysis development / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription ...adenohypophysis development / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Pituitary-specific positive transcription factor 1 / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. ...Pituitary-specific positive transcription factor 1 / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / lambda repressor-like DNA-binding domains / Homeobox domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Pituitary-specific positive transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsAgarwal, S. / Cho, T.Y.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Biochemical and structural characterization of a novel cooperative binding mode by Pit-1 with CATT repeats in the macrophage migration inhibitory factor promoter.
Authors: Agarwal, S. / Cho, T.Y.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Pituitary-specific positive transcription factor 1
A: Pituitary-specific positive transcription factor 1
C: DNA (5'-D(*CP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*GP*GP*A)-3')
D: DNA (5'-D(*CP*CP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*GP*T)-3')
E: Pituitary-specific positive transcription factor 1
F: Pituitary-specific positive transcription factor 1
G: DNA (5'-D(*CP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*GP*GP*A)-3')
H: DNA (5'-D(*CP*CP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)96,8048
Polymers96,8048
Non-polymers00
Water0
1
B: Pituitary-specific positive transcription factor 1
A: Pituitary-specific positive transcription factor 1
C: DNA (5'-D(*CP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*GP*GP*A)-3')
D: DNA (5'-D(*CP*CP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)48,4024
Polymers48,4024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-43 kcal/mol
Surface area20320 Å2
MethodPISA
2
E: Pituitary-specific positive transcription factor 1
F: Pituitary-specific positive transcription factor 1
G: DNA (5'-D(*CP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*GP*GP*A)-3')
H: DNA (5'-D(*CP*CP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)48,4024
Polymers48,4024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-42 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.415, 97.518, 85.093
Angle α, β, γ (deg.)90.00, 93.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pituitary-specific positive transcription factor 1 / / PIT-1 / Growth hormone factor 1 / GHF-1


Mass: 17759.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POU1F1, GHF1, PIT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28069
#2: DNA chain DNA (5'-D(*CP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*AP*TP*TP*CP*GP*GP*A)-3')


Mass: 6348.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*CP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*GP*GP*T)-3')


Mass: 6535.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.84 Å3/Da / Density % sol: 56.7 % / Description: Long rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, 17.5% (w/v) PEG 6000, 5%(v/v) MPD

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3.15→47.2 Å / Num. obs: 18198 / % possible obs: 95.92 % / Redundancy: 9.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2242 / Rpim(I) all: 0.07616 / Net I/σ(I): 10.57
Reflection shellResolution: 3.15→3.263 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5317 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1681 / CC1/2: 0.989 / Rpim(I) all: 0.2808 / % possible all: 87.13

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AU7

1au7


Resolution: 3.15→47.2 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 852 4.71 %5% were flagged by Ctruncate
Rwork0.2305 ---
obs0.2327 18100 95.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4194 1640 0 0 5834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056114
X-RAY DIFFRACTIONf_angle_d0.5878581
X-RAY DIFFRACTIONf_dihedral_angle_d15.2344207
X-RAY DIFFRACTIONf_chiral_restr0.035960
X-RAY DIFFRACTIONf_plane_restr0.003833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.34730.32471310.30422618X-RAY DIFFRACTION88
3.3473-3.60570.33611330.27572834X-RAY DIFFRACTION95
3.6057-3.96840.29071580.24082890X-RAY DIFFRACTION98
3.9684-4.54220.2641550.20962927X-RAY DIFFRACTION98
4.5422-5.72120.25981280.21712975X-RAY DIFFRACTION99
5.7212-47.20.2451470.20183004X-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)
18.6396-2.7901-0.40874.62890.8451.5235-0.1001-0.0297-0.87030.60210.23190.34090.5338-0.2219-0.20740.4877-0.0842-0.09690.24260.14850.4381-20.4906-17.569712.0803
24.6541-1.3994-0.53173.49730.18163.12040.13-0.7431-0.03970.83610.0897-0.55580.28730.1217-0.07630.304-0.0769-0.01860.1760.04740.2913-17.28-6.085913.7194
30.4752-0.1122-0.61840.49450.19361.40150.2346-0.17390.18160.049-0.03820.157-0.6082-0.089-0.02950.54160.22090.24410.4807-0.14240.6053-20.84811.38054.5609
42.03320.6893-0.63213.4584-2.26143.44230.15320.645-0.0179-0.6755-0.0642-0.2620.49650.84440.05840.19880.1021-0.0470.49730.00440.2089-7.9231-4.1791-13.5174
52.56290.5381-2.32814.12760.895.1262-0.4843-0.0711-0.1473-0.43090.32920.43880.41430.23170.08770.4358-0.1273-0.1180.1237-0.03180.4087-46.5932-14.416-6.4695
60.4184-0.11050.15931.36960.53650.940.0187-0.1254-0.08270.0485-0.05510.09780.7575-0.01890.00790.4123-0.05630.0719-0.1794-0.12750.3589-41.7102-12.3781-4.1184
70.74381.5269-0.37133.5319-0.69310.32310.5909-0.3010.26811.067-0.49220.27520.3062-0.3466-0.00890.5958-0.19440.00590.3731-0.11090.226-46.09672.65963.9997
88.9211-2.6389-0.184.08761.51052.51520.46370.59750.6552-1.4107-0.29410.0612-0.31060.0963-0.0720.529-0.01790.02590.15870.06930.549-36.901216.9381-11.3195
90.3216-0.1234-0.29770.1625-0.02090.4596-0.11510.02280.418-0.41760.20420.0504-0.3353-0.0079-0.04870.4012-0.3725-0.2132-0.1954-0.04210.9728-31.964322.8454-3.3413
103.0598-1.79860.61136.98932.65984.5418-0.13610.370.5304-0.20320.4565-0.8484-0.57240.2351-0.03450.1403-0.0082-0.02350.2897-0.03020.0215-35.51167.8763-7.0203
111.8636-0.35690.0632.03150.17790.5895-0.0842-0.6180.98530.13470.00020.0046-0.1879-0.31060.20920.27440.03130.00730.2668-0.04860.3739-41.90562.40811.3881
126.55152.21492.4873.104-0.39354.0886-0.07940.37390.54540.15630.0313-0.0863-0.12370.90230.140.29620.02320.00960.3958-0.00840.328-8.24730.95231.0328
136.8796-0.43550.59282.2608-1.41432.60110.47310.38670.3913-0.0821-0.24620.1483-0.1240.2247-0.10580.3379-0.0812-0.10330.2231-0.02130.4558-8.55530.76071.5676
143.30640.6805-3.58191.2232-0.53693.94080.31150.28550.31360.3160.23880.2775-0.6182-0.2113-0.35350.1766-0.0162-0.02110.2122-0.05640.3182-32.622-1.4627-1.5861
157.1353-1.8184-1.21891.77541.87142.5763-0.3846-0.02180.6297-1.16390.11461.49560.0653-1.0330.05830.4069-0.03-0.27210.3305-0.03690.8386-50.44115.32433.5436
160.46850.29580.51560.83120.43850.59080.16680.43190.0236-0.2549-0.0627-0.2081-0.49250.295-0.12860.33170.00860.38670.9919-0.0864-0.1203-11.600314.2025-60.1462
175.10441.7841.77695.8307-3.38135.7097-0.17010.36020.41710.14360.2346-0.0183-0.77090.83940.09960.2702-0.0578-0.0380.4585-0.04480.288-12.977824.8192-50.8298
187.6303-0.73531.39843.43311.62172.71170.31980.91970.7034-0.8809-0.09550.1952-0.2172-0.41920.02250.32290.05340.0070.6155-0.0150.0932-18.450619.2889-56.7919
190.94120.4594-0.0241.6082-0.26480.0336-0.2202-0.07550.18140.4466-0.0119-0.3715-0.5865-0.47810.30330.17470.0688-0.00320.5840.03860.4223-12.711819.2927-39.2572
203.01011.2117-2.00294.81351.46844.8163-0.0338-0.5957-1.4431-0.246-0.36630.40581.3457-0.9730.16580.4435-0.090.07690.45790.22980.5789-23.0604-0.3382-32.6194
213.90664.763.1368.34053.1653.36310.5212-1.5573-0.57991.3854-0.07240.79670.0131-1.3063-0.35090.3756-0.03720.02811.01430.26760.5016-27.37844.6244-23.3424
224.41791.3508-0.26113.454-3.85168.0158-0.3174-0.704-0.5066-0.18890.29580.38410.5729-0.5475-0.22980.18220.0286-0.0340.37680.01250.3355-24.07947.9842-39.0571
232.3509-1.2773-0.78470.81320.36270.33540.17810.5938-0.6247-0.72850.0813-0.310.40350.71140.05210.69560.40140.21131.3506-0.41670.62113.0792.278-46.0197
243.39641.06810.84144.0275-0.99252.8352-0.24440.3091-0.0277-0.48190.4459-0.48581.32681.0089-0.0920.58170.12420.09410.8796-0.18110.42948.44623.843-43.7084
250.5546-0.6866-0.06871.9592-0.54710.40250.0823-0.16690.2926-0.2689-0.0239-0.2532-0.21560.1511-0.06390.4995-0.00060.09190.7358-0.31510.531414.269516.9776-41.4314
262.44030.07051.65045.9675-0.60481.2355-0.2623-0.87720.54811.0995-0.05470.5606-0.58510.12640.39270.4831-0.0374-0.0911.1583-0.32840.32412.22621.4858-24.3004
270.81360.1953-0.47190.0438-0.10470.34840.0426-0.66940.739-0.0926-0.0011-0.6133-0.16780.5892-0.08820.4049-0.0004-0.01791.1513-0.06750.738117.490914.6185-37.7065
288.93486.81337.34829.49826.0199.2345-0.4917-0.54940.24670.62760.50130.2906-0.0971.1017-0.04910.43240.0519-0.03340.8429-0.06220.45261.699122.3133-40.2473
298.8418-2.46320.83754.2715-0.35410.8379-0.28660.54690.9180.08120.26910.1732-0.2018-0.8878-0.02110.36030.050.07320.75830.04630.5404-24.417617.8919-39.5906
305.61953.5404-2.99886.65080.99515.59260.1648-1.468-0.28850.36110.08940.1455-0.2271-2.2941-0.29990.4570.10240.05940.98260.12430.591-32.40414.4223-42.1897
312.716-2.76552.48713.9985-1.87892.6636-0.4204-1.21910.93080.3590.2775-0.40410.2931-0.65650.24630.3876-0.00030.05860.6454-0.1220.3988-16.22821.4862-38.1018
325.99692.8053-2.53295.1345-2.35646.8620.0904-0.6952-0.60210.7867-0.059-0.4511-0.79740.3817-0.0470.3540.1865-0.03050.8480.01630.3302-0.116513.9904-39.7867
339.7998-0.58954.06175.87541.08067.6611-0.8766-0.08341.61330.65650.5752-1.23090.44621.75830.33670.6612-0.1381-0.17691.3283-0.05180.725817.21522.2926-39.2759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'B' and (resid 23 through 73 )
3X-RAY DIFFRACTION3chain 'B' and (resid 74 through 99 )
4X-RAY DIFFRACTION4chain 'B' and (resid 100 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2 through 38 )
6X-RAY DIFFRACTION6chain 'A' and (resid 39 through 75 )
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 99 )
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 117 )
9X-RAY DIFFRACTION9chain 'A' and (resid 118 through 131 )
10X-RAY DIFFRACTION10chain 'A' and (resid 132 through 150 )
11X-RAY DIFFRACTION11chain 'C' and (resid 170 through 179 )
12X-RAY DIFFRACTION12chain 'C' and (resid 180 through 190 )
13X-RAY DIFFRACTION13chain 'D' and (resid 170 through 179 )
14X-RAY DIFFRACTION14chain 'D' and (resid 180 through 184 )
15X-RAY DIFFRACTION15chain 'D' and (resid 185 through 190 )
16X-RAY DIFFRACTION16chain 'E' and (resid 3 through 22 )
17X-RAY DIFFRACTION17chain 'E' and (resid 23 through 51 )
18X-RAY DIFFRACTION18chain 'E' and (resid 52 through 73 )
19X-RAY DIFFRACTION19chain 'E' and (resid 74 through 99 )
20X-RAY DIFFRACTION20chain 'E' and (resid 100 through 117 )
21X-RAY DIFFRACTION21chain 'E' and (resid 118 through 131 )
22X-RAY DIFFRACTION22chain 'E' and (resid 132 through 150 )
23X-RAY DIFFRACTION23chain 'F' and (resid 2 through 43 )
24X-RAY DIFFRACTION24chain 'F' and (resid 44 through 73 )
25X-RAY DIFFRACTION25chain 'F' and (resid 74 through 99 )
26X-RAY DIFFRACTION26chain 'F' and (resid 100 through 150 )
27X-RAY DIFFRACTION27chain 'G' and (resid 170 through 174 )
28X-RAY DIFFRACTION28chain 'G' and (resid 175 through 179 )
29X-RAY DIFFRACTION29chain 'G' and (resid 180 through 190 )
30X-RAY DIFFRACTION30chain 'H' and (resid 170 through 174 )
31X-RAY DIFFRACTION31chain 'H' and (resid 175 through 179 )
32X-RAY DIFFRACTION32chain 'H' and (resid 180 through 184 )
33X-RAY DIFFRACTION33chain 'H' and (resid 185 through 189 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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