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- PDB-2vi6: Crystal Structure of the Nanog Homeodomain -

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Basic information

Entry
Database: PDB / ID: 2vi6
TitleCrystal Structure of the Nanog Homeodomain
ComponentsHOMEOBOX PROTEIN NANOG
KeywordsTRANSCRIPTION / HOMEODOMAIN / DNA-BINDING / TRANSCRIPTION FACTOR / DEVELOPMENTAL PROTEIN / TRANSCRIPTION REGULATION / NANOG / NUCLEUS / HOMEOBOX / ACTIVATOR / REPRESSOR
Function / homology
Function and homology information


negative regulation of endodermal cell fate specification / negative regulation of cell fate commitment / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / mesodermal cell fate commitment / cellular response to erythropoietin / cellular response to rapamycin / multidimensional cell growth / cell dedifferentiation / regulation of stem cell division / endodermal cell fate specification ...negative regulation of endodermal cell fate specification / negative regulation of cell fate commitment / RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity / mesodermal cell fate commitment / cellular response to erythropoietin / cellular response to rapamycin / multidimensional cell growth / cell dedifferentiation / regulation of stem cell division / endodermal cell fate specification / gonad development / tissue regeneration / stem cell division / embryonic pattern specification / stem cell population maintenance / positive regulation of stem cell proliferation / regulation of cell differentiation / somatic stem cell population maintenance / negative regulation of cell differentiation / transcription factor binding / negative regulation of BMP signaling pathway / cis-regulatory region sequence-specific DNA binding / response to retinoic acid / positive regulation of mitotic cell cycle / response to organic substance / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of cell population proliferation / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein NANOG
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJauch, R. / Ng, C.K.L. / Saitakendu, K.S. / Stevens, R.C. / Kolatkar, P.R.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog.
Authors: Jauch, R. / Ng, C.K.L. / Saitakendu, K.S. / Stevens, R.C. / Kolatkar, P.R.
History
DepositionNov 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOMEOBOX PROTEIN NANOG
B: HOMEOBOX PROTEIN NANOG
C: HOMEOBOX PROTEIN NANOG
D: HOMEOBOX PROTEIN NANOG
E: HOMEOBOX PROTEIN NANOG
F: HOMEOBOX PROTEIN NANOG
G: HOMEOBOX PROTEIN NANOG
H: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)60,8088
Polymers60,8088
Non-polymers00
Water1,24369
1
A: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)7,6011
Polymers7,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)7,6011
Polymers7,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)7,6011
Polymers7,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)7,6011
Polymers7,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)7,6011
Polymers7,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)7,6011
Polymers7,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)7,6011
Polymers7,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: HOMEOBOX PROTEIN NANOG


Theoretical massNumber of molelcules
Total (without water)7,6011
Polymers7,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.318, 114.771, 62.771
Angle α, β, γ (deg.)90.00, 98.68, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.296178, -0.828859, -0.474628), (0.831273, -0.021035, 0.555467), (-0.470387, -0.559062, 0.682778)77.8993, -23.2391, 70.5943
2given(-0.725684, -0.446251, 0.523682), (0.686929, -0.426914, 0.58811), (-0.038878, 0.786515, 0.616347)48.6592, 25.0729, -33.8704
3given(0.850005, 0.21907, -0.479061), (0.362741, -0.902871, 0.230743), (-0.381982, -0.369908, -0.846911)30.6891, 70.1292, 128.1162
4given(0.036894, -0.324991, -0.944997), (-0.321237, 0.891594, -0.319167), (0.94628, 0.315343, -0.071504)116.2694, 0.8116, 2.1429
5given(-0.312064, 0.790285, 0.527319), (0.869375, 0.013697, 0.493963), (0.383149, 0.612587, -0.691328)-67.5347, 8.9067, 36.7058
6given(-0.301956, 0.494814, 0.814851), (-0.737174, 0.420785, -0.528692), (-0.604481, -0.760328, 0.237705)-27.2745, 38.7219, 84.2503
7given(-0.320536, 0.054304, -0.945679), (-0.017064, -0.998524, -0.051555), (-0.947083, -0.000388, 0.32099)52.2564, 123.903, 42.4374

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Components

#1: Protein
HOMEOBOX PROTEIN NANOG / / HOMEOBOX TRANSCRIPTION FACTOR NANOG / EARLY EMBRYO SPECIFIC EXPRESSION NK-TYPE HOMEOBOX PROTEIN / ...HOMEOBOX TRANSCRIPTION FACTOR NANOG / EARLY EMBRYO SPECIFIC EXPRESSION NK-TYPE HOMEOBOX PROTEIN / ES CELL- ASSOCIATED PROTEIN 4 / NANOG


Mass: 7600.954 Da / Num. of mol.: 8 / Fragment: HOMEODOMAIN, RESIDUES 96-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETG60A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q80Z64
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGT DIPEPTIDE DERVIED FROM THE EXPRESSION VECTOR

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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: 3.09 Å3/Da / Density % sol: 60.2 % / Description: DNA REMOVED FROM STARTING MODEL
Crystal growpH: 7 / Details: PEG3350, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20786 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / % possible all: 68.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IG7

1ig7


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / SU B: 23.396 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.571 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FIRST 7 N-TERMINAL RESIDUES DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1040 5 %RANDOM
Rwork0.221 ---
obs0.223 19601 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.73 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å2-2.23 Å2
2---2.7 Å20 Å2
3---4.26 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3763 0 0 69 3832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.935106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7775429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90824.8200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61115829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8731524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022772
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21560
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22605
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3990.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4851.52250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87823493
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23131846
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9714.51613
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.398 63
Rwork0.36 1094
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)
12.70971.82040.014511.1122-3.46165.79430.02190.00390.199-0.0098-0.00980.037-0.19670.141-0.0121-0.0612-0.00180.0373-0.1902-0.036-0.077620.897236.89643.0032
216.84812.39350.4261.2269-0.93472.14030.0232-0.6510.01230.1054-0.07850.0162-0.08620.13280.0553-0.1019-0.0342-0.0591-0.0489-0.041-0.024346.110961.629741.5968
37.4803-3.12640.616516.1526-0.17411.1416-0.05810.1330.35140.69010.2187-0.2114-0.003-0.0404-0.1606-0.0881-0.00270.0801-0.14230.0304-0.075725.289367.815939.8445
410.985-3.58568.14216.1674-2.304811.54850.73610.3318-1.0742-0.0879-0.10950.22430.7363-0.1368-0.6266-0.0909-0.0288-0.0801-0.1286-0.0642-0.067712.141159.431369.2244
520.697-5.00169.75489.2223-1.82826.7508-0.72730.51521.2150.7847-0.0284-1.0327-0.31790.1860.7557-0.07440.0223-0.0271-0.17150.0399-0.134523.419776.159775.8197
611.86581.8271.5016.9012-0.831111.0460.15031.07690.3064-0.30250.05940.1477-0.03570.1972-0.2096-0.26060.05010.00270.14570.0802-0.2078-0.838374.090856.1177
75.6802-0.57741.100319.3998-4.51015.319-0.15490.34430.2525-0.91660.35670.78890.0611-0.2538-0.2018-0.1135-0.1086-0.0666-0.10050.10980.059111.733354.417130.4267
812.28370.687-5.26436.3878-0.29497.55150.2392-0.18570.1050.2110.17020.6561-0.3055-0.5742-0.4095-0.05990.11220.1353-0.15160.25390.001811.201685.168834.3696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 60
2X-RAY DIFFRACTION2B7 - 60
3X-RAY DIFFRACTION3C6 - 60
4X-RAY DIFFRACTION4D6 - 60
5X-RAY DIFFRACTION5E7 - 60
6X-RAY DIFFRACTION6F6 - 60
7X-RAY DIFFRACTION7G6 - 60
8X-RAY DIFFRACTION8H7 - 60

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