[English] 日本語
Yorodumi
- PDB-6el8: Crystal structure of the Forkhead domain of human FOXN1 in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6el8
TitleCrystal structure of the Forkhead domain of human FOXN1 in complex with DNA
Components
  • DNA (5'-D(*GP*GP*TP*GP*GP*CP*GP*TP*CP*TP*TP*CP*A)-3')
  • DNA (5'-D(*TP*GP*AP*AP*GP*AP*CP*GP*CP*CP*AP*CP*C)-3')
  • Forkhead box protein N1
KeywordsDNA BINDING PROTEIN / FOXN1 / Thumus / transcription factor / Structural Genomics / Structural Genomics Consortium / SGC
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
DNA / DNA (> 10) / Forkhead box protein N1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsNewman, J.A. / Aitkenhead, H.A. / Pinkas, D.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. / Structural Genomics Consortium (SGC)
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 in complex with DNA
Authors: Newman, J.A. / Aitkenhead, H.A. / Pinkas, D.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionSep 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 2.0Feb 28, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations
Category: atom_site / pdbx_struct_sheet_hbond ...atom_site / 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 / _pdbx_struct_sheet_hbond.range_1_auth_seq_id ..._atom_site.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 3.0Apr 11, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / pdbx_poly_seq_scheme ...atom_site / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _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.auth_seq_id / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 3.1Jan 17, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Forkhead box protein N1
B: DNA (5'-D(*GP*GP*TP*GP*GP*CP*GP*TP*CP*TP*TP*CP*A)-3')
C: DNA (5'-D(*TP*GP*AP*AP*GP*AP*CP*GP*CP*CP*AP*CP*C)-3')
D: Forkhead box protein N1
E: DNA (5'-D(*GP*GP*TP*GP*GP*CP*GP*TP*CP*TP*TP*CP*A)-3')
F: DNA (5'-D(*TP*GP*AP*AP*GP*AP*CP*GP*CP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)38,9376
Polymers38,9376
Non-polymers00
Water5,639313
1
A: Forkhead box protein N1
B: DNA (5'-D(*GP*GP*TP*GP*GP*CP*GP*TP*CP*TP*TP*CP*A)-3')
C: DNA (5'-D(*TP*GP*AP*AP*GP*AP*CP*GP*CP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)19,4693
Polymers19,4693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-21 kcal/mol
Surface area9290 Å2
MethodPISA
2
D: Forkhead box protein N1
E: DNA (5'-D(*GP*GP*TP*GP*GP*CP*GP*TP*CP*TP*TP*CP*A)-3')
F: DNA (5'-D(*TP*GP*AP*AP*GP*AP*CP*GP*CP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)19,4693
Polymers19,4693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-19 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.848, 43.284, 58.317
Angle α, β, γ (deg.)90.05, 95.67, 93.77
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 11524.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: First two residues remain from cleavage of purification tag
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXN1, RONU, WHN / Production host: Escherichia coli (E. coli) / References: UniProt: O15353
#2: DNA chain DNA (5'-D(*GP*GP*TP*GP*GP*CP*GP*TP*CP*TP*TP*CP*A)-3')


Mass: 3998.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*GP*AP*AP*GP*AP*CP*GP*CP*CP*AP*CP*C)-3')


Mass: 3945.589 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 8% Peg 4000, 0.1M Acetate pH4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.61→34.52 Å / Num. obs: 44332 / % possible obs: 90.7 % / Redundancy: 2.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.028 / Net I/σ(I): 8.1
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1937 / CC1/2: 0.963 / Rpim(I) all: 0.333 / % possible all: 53.4

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCN

5ocn


Resolution: 1.61→34 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.77
RfactorNum. reflection% reflection
Rfree0.2394 2080 4.75 %
Rwork0.1938 --
obs0.1959 43746 89.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.61→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 1054 0 313 2809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152674
X-RAY DIFFRACTIONf_angle_d1.4743824
X-RAY DIFFRACTIONf_dihedral_angle_d21.4561410
X-RAY DIFFRACTIONf_chiral_restr0.077414
X-RAY DIFFRACTIONf_plane_restr0.01300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6097-1.64720.431810.40891502X-RAY DIFFRACTION49
1.6472-1.68840.4302870.37761912X-RAY DIFFRACTION61
1.6884-1.7340.39531380.36542530X-RAY DIFFRACTION82
1.734-1.78510.3871580.35112801X-RAY DIFFRACTION91
1.7851-1.84270.37911700.30672894X-RAY DIFFRACTION93
1.8427-1.90850.34061420.2852926X-RAY DIFFRACTION95
1.9085-1.98490.27871550.25362958X-RAY DIFFRACTION95
1.9849-2.07530.2961280.24843013X-RAY DIFFRACTION96
2.0753-2.18470.29941410.22392981X-RAY DIFFRACTION97
2.1847-2.32150.27011350.2153030X-RAY DIFFRACTION97
2.3215-2.50070.25841560.20152989X-RAY DIFFRACTION97
2.5007-2.75230.25761550.19873005X-RAY DIFFRACTION97
2.7523-3.15030.25441360.20393058X-RAY DIFFRACTION98
3.1503-3.96810.20071330.15733037X-RAY DIFFRACTION97
3.9681-34.53190.16991650.13683030X-RAY DIFFRACTION98

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more