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- PDB-6nce: Crystal structure of the human FOXN3 DNA binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6nce
TitleCrystal structure of the human FOXN3 DNA binding domain in complex with a forkhead DNA sequence
Components
  • DNA (5'-D(*AP*CP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*TP*AP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*TP*AP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3')
  • Forkhead box protein N3FOX proteins
KeywordsDNA BINDING PROTEIN/DNA / sequence specific DNA binding / regulation of transcription DNA templated / DNA Binding Transcription Factor Activity / forkhead / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


craniofacial suture morphogenesis / : / mitotic G2 DNA damage checkpoint signaling / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein N3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsRogers, J.M. / Jarrett, S.M. / Seegar, T.C. / Waters, C.T. / Hallworth, A.N. / Blacklow, S.C. / Bulyk, M.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HG003985 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA220340 United States
CitationJournal: Mol. Cell / Year: 2019
Title: Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes.
Authors: Rogers, J.M. / Waters, C.T. / Seegar, T.C.M. / Jarrett, S.M. / Hallworth, A.N. / Blacklow, S.C. / Bulyk, M.L.
History
DepositionDec 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
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_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Forkhead box protein N3
C: DNA (5'-D(*TP*CP*TP*TP*AP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3')
D: DNA (5'-D(*AP*CP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*TP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6116
Polymers21,4703
Non-polymers1413
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Protein Binding Microarray
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-37 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.940, 102.080, 34.450
Angle α, β, γ (deg.)90.00, 102.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-411-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Forkhead box protein N3 / FOX proteins / Checkpoint suppressor 1


Mass: 11677.499 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXN3, C14orf116, CHES1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00409

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*TP*CP*TP*TP*AP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3')


Mass: 4905.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*TP*AP*AP*G)-3')


Mass: 4887.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 22 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 0.1 M BisTris pH 5.4, 0.2 M MgCl2, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.598→30.57 Å / Num. obs: 9664 / % possible obs: 96.62 % / Redundancy: 3.5 % / Biso Wilson estimate: 85.51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.04832 / Rpim(I) all: 0.03054 / Rrim(I) all: 0.05745 / Net I/σ(I): 12.6
Reflection shellResolution: 2.598→2.691 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.328 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 958 / CC1/2: 0.563 / Rpim(I) all: 0.8254 / Rrim(I) all: 1.569 / % possible all: 94.47

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C6Y

2c6y


Resolution: 2.598→30.57 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 42.1
RfactorNum. reflection% reflection
Rfree0.2706 957 9.98 %
Rwork0.2346 --
obs-9590 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms731 650 8 19 1408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041487
X-RAY DIFFRACTIONf_angle_d0.5422146
X-RAY DIFFRACTIONf_dihedral_angle_d22.176768
X-RAY DIFFRACTIONf_chiral_restr0.029232
X-RAY DIFFRACTIONf_plane_restr0.003160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5975-2.73440.49931310.45341208X-RAY DIFFRACTION95
2.7344-2.90560.45541420.3981264X-RAY DIFFRACTION98
2.9056-3.12980.43291360.34141236X-RAY DIFFRACTION98
3.1298-3.44450.31921330.26831204X-RAY DIFFRACTION94
3.4445-3.94210.27331380.21141228X-RAY DIFFRACTION98
3.9421-4.96380.22131370.20021245X-RAY DIFFRACTION97
4.9638-32.32970.23671400.20051251X-RAY DIFFRACTION97
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)
16.90212.4576-4.23075.8399-5.18257.39691.3373-1.83760.4150.6285-0.8365-0.0191-2.45270.4522-0.60821.4618-0.2705-0.08980.972-0.09280.6495121.22944.882847.1142
29.8024-4.8584-4.12389.18752.35662.5975-0.4093-0.4853-1.5540.26570.22570.63552.24340.94020.0581.0724-0.0364-0.12950.7980.09010.7703125.295-4.576844.2123
36.1684-5.07063.11419.6351-3.1791.93181.2688-0.5227-0.4393-0.2004-0.3011.3013-2.3375-0.0306-0.81781.2997-0.249-0.1570.7122-0.01540.7075113.6571-0.943444.3614
43.6294-2.2615-3.16225.6852-3.23729.05330.3477-1.4179-1.3304-0.45221.06591.9633-0.72510.2374-1.89520.5853-0.2235-0.06170.98250.01420.7954123.74732.588631.5908
55.98483.7643-2.32395.5218-4.58554.017-0.6607-0.1436-1.5133-3.72850.9373-0.7745-1.9996-0.1826-0.45681.34080.069-0.00080.7055-0.24860.8086127.3599-4.105732.3108
69.6162-4.3479-5.70395.20635.41435.81691.69560.01882.2578-2.62661.22040.9432-3.04271.2612-2.68511.6029-0.38180.24890.82730.0531.5313127.27812.847339.6896
76.0437-4.0463-4.25184.17432.77737.1993-2.26711.4635-2.619-4.75470.01786.18750.5765-0.61531.8193.03770.0599-0.57221.03140.272.3868109.90421.144432.0461
87.9083-5.3918-2.77828.5908-3.41418.3430.41350.9111-1.2205-1.9721-1.20381.64650.9756-0.80220.90311.58-0.1195-0.09060.7393-0.09791.1632108.7901-4.34233.65
98.7381-3.2876-1.20787.81377.03456.04020.31381.4795-1.33220.1933-0.40281.0856-0.2042-0.1868-0.13161.20270.1542-0.27610.8141-0.21991.1184110.4625-8.673732.6462
103.84043.76294.79934.36784.48865.9835-1.5351-1.53733.4256-2.0202-1.51541.642-3.4031-0.15682.6222.09470.009-0.04991.16340.14631.609106.111916.265639.2676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 111 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 147 )
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 168 )
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 175 )
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 192 )
6X-RAY DIFFRACTION6chain 'A' and (resid 193 through 207 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 5 )
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 16 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 10 )
10X-RAY DIFFRACTION10chain 'D' and (resid 11 through 16 )

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