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- PDB-5ocn: Crystal structure of the forkhead domain of human FOXN1 -

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Basic information

Entry
Database: PDB / ID: 5ocn
TitleCrystal structure of the forkhead domain of human FOXN1
ComponentsForkhead box protein N1FOX proteins
KeywordsTRANSCRIPTION / Forkhead domain / thymus / transcription factor
Function / homology
Function and homology information


regulation of positive thymic T cell selection / lymphoid lineage cell migration into thymus / thymus epithelium morphogenesis / positive regulation of epithelial cell differentiation / nail development / positive regulation of hair follicle development / blood vessel morphogenesis / T cell lineage commitment / T cell homeostasis / hair follicle development ...regulation of positive thymic T cell selection / lymphoid lineage cell migration into thymus / thymus epithelium morphogenesis / positive regulation of epithelial cell differentiation / nail development / positive regulation of hair follicle development / blood vessel morphogenesis / T cell lineage commitment / T cell homeostasis / hair follicle development / epidermis development / keratinocyte differentiation / animal organ morphogenesis / defense response / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / 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 ...: / 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
: / Forkhead box protein N1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Pinkas, D.M. / von Delft, F. / Arrowsmith, C.H. / Edwwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To be published
Title: Crystal structure of the forkhead domain of human FOXN1
Authors: Newman, J.A. / Aitkenhead, H. / Pinkas, D.M. / von Delft, F. / Arrowsmith, C.H. / Edwwards, A. / Bountra, C. / Gileadi, O.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 2.0Feb 28, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Forkhead box protein N1
B: Forkhead box protein N1
C: Forkhead box protein N1
D: Forkhead box protein N1
E: Forkhead box protein N1
F: Forkhead box protein N1
G: Forkhead box protein N1
H: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,50816
Polymers92,1958
Non-polymers3138
Water36020
1
A: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,5241
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,5241
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,5241
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,5241
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,5241
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,5241
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,5241
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Forkhead box protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,5241
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.141, 78.203, 263.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Forkhead box protein N1 / FOX proteins / Winged-helix transcription factor nude


Mass: 11524.400 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXN1, RONU, WHN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O15353
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 32 % PEG 3350, 0.25 M Potassium Citrate tribasic, 10% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→43.92 Å / Num. obs: 24950 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.044 / Net I/σ(I): 11.8
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.321 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3240 / CC1/2: 0.876 / Rpim(I) all: 0.713 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c6y
Resolution: 2.7→43.913 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.18
RfactorNum. reflection% reflection
Rfree0.2838 1269 5.12 %
Rwork0.2511 --
obs0.2527 24773 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→43.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5307 0 8 20 5335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025458
X-RAY DIFFRACTIONf_angle_d0.4637384
X-RAY DIFFRACTIONf_dihedral_angle_d11.883235
X-RAY DIFFRACTIONf_chiral_restr0.036789
X-RAY DIFFRACTIONf_plane_restr0.003915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80810.46041430.39392583X-RAY DIFFRACTION99
2.8081-2.93590.39611130.33432524X-RAY DIFFRACTION99
2.9359-3.09060.32771540.30472532X-RAY DIFFRACTION98
3.0906-3.28420.29391320.28812605X-RAY DIFFRACTION100
3.2842-3.53770.29311430.27772588X-RAY DIFFRACTION100
3.5377-3.89350.30891300.23662598X-RAY DIFFRACTION100
3.8935-4.45640.26021490.22752602X-RAY DIFFRACTION99
4.4564-5.61280.24371570.22062665X-RAY DIFFRACTION100
5.6128-43.9190.26991480.23612807X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.80481.32950.60713.589-0.88763.7826-0.0611-0.38360.12690.09590.29110.4725-0.1266-0.4415-0.23470.37110.0460.04220.44270.08520.47412.0243-1.4826-57.6107
24.60630.7971-3.03576.376-2.61837.8403-0.019-0.1582-0.3276-0.2911-0.341-0.6033-0.11430.29920.3250.42810.0202-0.00820.38840.04460.485423.11733.9129-73.5848
34.49070.4203-0.35244.83362.44736.05510.12630.0849-0.09160.297-0.07420.2545-0.1588-0.021-0.03570.45890.07520.07240.45080.03350.4997.902-9.4648-40.7406
45.30431.27960.32832.3709-0.04488.4521-0.0953-0.083-0.49220.08770.0263-0.07591.43260.15220.15840.86290.01810.08690.4389-0.010.522820.6616-6.9385-90.5615
53.06531.04860.21595.41940.94728.95750.06650.8130.0824-0.39890.09820.4253-0.2932-1.4382-0.12430.89840.0108-0.00361.15640.00290.61942.86714.0993-105.9241
65.3247-2.7085-2.1535.8225-1.42544.46210.2785-0.2940.59610.3669-0.2141-0.3106-0.5995-0.61870.0871.2338-0.0136-0.15930.8347-0.01440.70210.713710.3712-123.269
73.73790.2536-0.05285.72081.14256.50460.0715-0.3289-0.61690.7144-0.16270.26851.0108-0.70940.03041.0865-0.21180.05140.72790.10170.57322.8828-8.1297-155.8463
84.36752.9363-0.31154.7028-0.41065.22680.48140.074-0.33760.4421-0.3723-0.19931.3740.3821-0.13721.41310.1013-0.11040.69490.06030.578414.4489-10.0097-139.4897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 270 through 363)
2X-RAY DIFFRACTION2(chain 'B' and resid 270 through 363)
3X-RAY DIFFRACTION3(chain 'C' and resid 272 through 363)
4X-RAY DIFFRACTION4(chain 'D' and resid 274 through 362)
5X-RAY DIFFRACTION5(chain 'E' and resid 272 through 361)
6X-RAY DIFFRACTION6(chain 'F' and resid 270 through 361)
7X-RAY DIFFRACTION7(chain 'G' and resid 275 through 362)
8X-RAY DIFFRACTION8(chain 'H' and resid 275 through 362)

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