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- PDB-4rbo: Crystal structure of a Nanog homeobox (NANOG) from Homo sapiens a... -

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Basic information

Entry
Database: PDB / ID: 4rbo
TitleCrystal structure of a Nanog homeobox (NANOG) from Homo sapiens at 3.30 A resolution
Components
  • 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3'
  • 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3'
  • Putative homeobox protein NANOGP8
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION/DNA / Homeobox / PF00046 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Partnership for Stem Cell Biology / STEMCELL / Protein Structure Initiative / PSI-BIOLOGY / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal cell fate specification / Specification of primordial germ cells / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cell cycle G1/S phase transition / Transcriptional regulation of pluripotent stem cells / Germ layer formation at gastrulation / stem cell population maintenance / positive regulation of stem cell proliferation ...POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal cell fate specification / Specification of primordial germ cells / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cell cycle G1/S phase transition / Transcriptional regulation of pluripotent stem cells / Germ layer formation at gastrulation / stem cell population maintenance / positive regulation of stem cell proliferation / regulation of cell differentiation / somatic stem cell population maintenance / 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 / Interleukin-4 and Interleukin-13 signaling / cell differentiation / transcription cis-regulatory region 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 / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / 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
DNA / DNA (> 10) / Homeobox protein NANOGP8 / Homeobox protein NANOG
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells.
Authors: Hayashi, Y. / Caboni, L. / Das, D. / Yumoto, F. / Clayton, T. / Deller, M.C. / Nguyen, P. / Farr, C.L. / Chiu, H.J. / Miller, M.D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. ...Authors: Hayashi, Y. / Caboni, L. / Das, D. / Yumoto, F. / Clayton, T. / Deller, M.C. / Nguyen, P. / Farr, C.L. / Chiu, H.J. / Miller, M.D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Tomoda, K. / Conklin, B.R. / Wilson, I.A. / Yamanaka, S. / Fletterick, R.J.
History
DepositionSep 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative homeobox protein NANOGP8
B: 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3'
C: 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3'
D: Putative homeobox protein NANOGP8
E: 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3'
F: 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)31,8736
Polymers31,8736
Non-polymers00
Water0
1
A: Putative homeobox protein NANOGP8
B: 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3'
C: 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)15,9373
Polymers15,9373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-21 kcal/mol
Surface area7730 Å2
MethodPISA
2
D: Putative homeobox protein NANOGP8
E: 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3'
F: 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)15,9373
Polymers15,9373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-19 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.603, 215.603, 42.269
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative homeobox protein NANOGP8 /


Mass: 8610.933 Da / Num. of mol.: 2 / Fragment: UNP residues 94-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NANOGP8, NM_024865 / Plasmid: 46EkTevLIC / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q6NSW7, UniProt: Q9H9S0*PLUS
#2: DNA chain 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3'


Mass: 3647.393 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3'


Mass: 3678.403 Da / Num. of mol.: 2 / Source method: obtained synthetically
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MAHHHHHHVDDDDKMSENLYFQ. THE TAG ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MAHHHHHHVDDDDKMSENLYFQ. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 94-162 OF THE TARGET SEQUENCE.

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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: 4.45 Å3/Da / Density % sol: 72.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.66
Details: 0.200M calcium acetate, 12.00% 2-propanol, 0.1M sodium cacodylate pH 5.66, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→29.899 Å / Num. all: 8834 / Num. obs: 8834 / % possible obs: 97 % / Redundancy: 3.4 % / Rsym value: 0.083 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allRsym value% possible all
3.3-3.393.20.55219396020.55294.3
3.39-3.483.60.42622756390.42697.2
3.48-3.583.60.48921966130.48998.6
3.58-3.693.70.35321615820.35399.1
3.69-3.813.80.26821195650.26896
3.81-3.943.60.27519075370.27596.1
3.94-4.093.30.22216564960.22293.2
4.09-4.263.20.13717615420.13798.7
4.26-4.453.60.14218365040.142100
4.45-4.673.50.11217715050.11299.6
4.67-4.923.30.10815404670.10899.7
4.92-5.223.50.07715654440.07797
5.22-5.583.30.06312063710.06391.5
5.58-6.033.50.06914164090.06999.3
6.03-6.63.60.07212883610.07299.4
6.6-7.383.50.05511773350.05597.5
7.38-8.522.90.0418192830.04191.1
8.52-10.443.10.048202620.0499.1
10.44-14.763.10.0376492100.03798.7
14.76-29.8992.80.023011070.0282.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
SCALA3.3.20data scaling
PHENIX(phenix.refine:refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→29.899 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.48 / σ(F): 1.34 / Phase error: 30.15 / Stereochemistry target values: ML
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflection
Rfree0.2682 417 4.73 %
Rwork0.2349 --
obs0.2365 8823 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 325.04 Å2 / Biso mean: 188.3153 Å2 / Biso min: 76.41 Å2
Refinement stepCycle: LAST / Resolution: 3.3→29.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 972 0 0 1904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032036
X-RAY DIFFRACTIONf_angle_d0.7782938
X-RAY DIFFRACTIONf_chiral_restr0.036325
X-RAY DIFFRACTIONf_plane_restr0.002207
X-RAY DIFFRACTIONf_dihedral_angle_d23.088830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 96 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3003-3.77710.31111530.280427032856
3.7771-4.75560.29351370.267627632900
4.7556-29.90.23931270.207929403067
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)
10.39140.7958-1.60960.6299-1.3963.4839-0.32750.36940.4547-0.62810.22150.11441.5177-0.5774-0.00820.94850.1095-0.22821.27230.01351.042121.2803110.51446.7518
21.46470.9129-2.45380.2148-1.56563.4663-0.55460.61710.5751-0.11870.37360.4921-1.07880.2675-0.00050.7894-0.1378-0.21920.97740.10461.1227124.8855123.225840.6024
31.91681.1172-2.96010.0404-1.84934.03480.0137-1.51230.5008-0.81170.57760.4078-1.40290.29910.25631.4261-0.1448-0.41130.72210.03851.4195124.6114123.196839.023
42.55780.6461.473.07811.61770.5826-1.51640.19080.2798-0.75821.054-0.49851.4063-0.3094-0.00112.0677-0.11770.03191.61450.06030.979122.044499.800725.7571
51.2662-1.4691.21161.332-0.88240.3969-1.2382-0.3223-1.61230.55530.46350.97731.69060.80960.00011.64530.28920.09751.3955-0.04751.7822123.000585.802931.0926
60.3115-0.52270.29610.0014-0.1807-0.0503-0.4334-1.0354-1.85120.1070.5401-0.84080.96980.8207-0.00122.7525-0.12150.48761.90180.24742.0894123.215986.031132.8668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 100 through 154)A0
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 12)B0
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 12)C0
4X-RAY DIFFRACTION4chain 'D' and (resid 100 through 153)D0
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 12)E0
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 12)F0

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