[English] 日本語
Yorodumi
- PDB-8byx: HOXB13-homodimer bound to DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8byx
TitleHOXB13-homodimer bound to DNA
Components
  • (DNA) x 2
  • Homeobox protein Hox-B13
KeywordsTRANSCRIPTION / transcription factor / DNA-binding protein / protein-DNA complex
Function / homology
Function and homology information


epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / response to testosterone / epidermis development / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / angiogenesis ...epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / response to testosterone / epidermis development / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / angiogenesis / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Homeobox protein Hox1A3 N-terminal / : / Hox protein A13 N terminal / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein Hox-B13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMorgunova, E. / Popov, A. / Yin, Y. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2025
Title: DNA-guided transcription factor interactions extend human gene regulatory code.
Authors: Xie, Z. / Sokolov, I. / Osmala, M. / Yue, X. / Bower, G. / Pett, J.P. / Chen, Y. / Wang, K. / Cavga, A.D. / Popov, A. / Teichmann, S.A. / Morgunova, E. / Kvon, E.Z. / Yin, Y. / Taipale, J.
History
DepositionDec 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: DNA
E: DNA
B: Homeobox protein Hox-B13
C: DNA
F: DNA
A: Homeobox protein Hox-B13
H: DNA
I: DNA
G: Homeobox protein Hox-B13
J: Homeobox protein Hox-B13
K: Homeobox protein Hox-B13
L: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)78,49512
Polymers78,49512
Non-polymers00
Water34219
1
D: DNA
E: DNA
B: Homeobox protein Hox-B13
J: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)26,1654
Polymers26,1654
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA
F: DNA
A: Homeobox protein Hox-B13
K: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)26,1654
Polymers26,1654
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: DNA
I: DNA
G: Homeobox protein Hox-B13
L: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)26,1654
Polymers26,1654
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.779, 116.779, 118.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-302-

HOH

21G-301-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515
1616
1717
1818
1919
2020
2121

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

-
Components

#1: DNA chain DNA


Mass: 5518.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA


Mass: 5510.635 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein
Homeobox protein Hox-B13


Mass: 7567.932 Da / Num. of mol.: 6 / Fragment: UNP residues 217-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOXB13 / Plasmid: pETG20A-SBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q92826
#4: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density meas: 67 Mg/m3 / Density % sol: 53.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 24 % PEG 1500 MME, 0.15M potassium chloride, 0.05M Tris-HCl buffer, 2%PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.91→59.03 Å / Num. obs: 18396 / % possible obs: 99.5 % / Redundancy: 7.5 % / CC1/2: 0.995 / Rpim(I) all: 0.05 / Rrim(I) all: 0.134 / Net I/σ(I): 8.6 / Num. measured all: 138874
Reflection shellResolution: 2.91→3.07 Å / % possible obs: 96.9 % / Redundancy: 7.8 % / Num. measured all: 19863 / Num. unique obs: 2551 / CC1/2: 0.323 / Rpim(I) all: 1.458 / Rrim(I) all: 4.116 / Net I/σ(I) obs: 0.7

-
Processing

Software
NameVersionClassification
REFMAC5refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 36.603 / SU ML: 0.61 / Cross valid method: THROUGHOUT / ESU R Free: 0.532 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30432 840 5 %RANDOM
Rwork0.2539 ---
obs0.25635 16051 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 116.374 Å2
Baniso -1Baniso -2Baniso -3
1--4.38 Å20 Å20 Å2
2---4.38 Å20 Å2
3---8.75 Å2
Refinement stepCycle: 1 / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 2198 0 19 5226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125648
X-RAY DIFFRACTIONr_bond_other_d0.0020.0184402
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.447887
X-RAY DIFFRACTIONr_angle_other_deg1.2782.00110241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg27.6066.742980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72318.492179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.56115639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4151547
X-RAY DIFFRACTIONr_chiral_restr0.1780.233809
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024546
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021242
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.91113.3681418
X-RAY DIFFRACTIONr_mcbond_other8.87413.3681417
X-RAY DIFFRACTIONr_mcangle_it14.31220.031762
X-RAY DIFFRACTIONr_mcangle_other14.31520.0331763
X-RAY DIFFRACTIONr_scbond_it8.73111.224230
X-RAY DIFFRACTIONr_scbond_other8.7311.2214231
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.15816.7216126
X-RAY DIFFRACTIONr_long_range_B_refined18.44418457
X-RAY DIFFRACTIONr_long_range_B_other18.44418458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D15910.08
12C15910.08
21D15660.11
22H15660.11
31E17100.03
32F17100.03
41E16770.06
42I16770.06
51B18170.11
52A18170.11
61B18460.13
62G18460.13
71B17990.09
72J17990.09
81B18810.1
82K18810.1
91B15160.14
92L15160.14
101C16260.08
102H16260.08
111F16840.06
112I16840.06
121A18200.1
122G18200.1
131A17840.11
132J17840.11
141A18250.1
142K18250.1
151A14980.16
152L14980.16
161G17630.11
162J17630.11
171G18730.12
172K18730.12
181G14980.16
182L14980.16
191J18080.09
192K18080.09
201J15100.15
202L15100.15
211K15100.14
212L15100.14
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 86 -
Rwork0.518 1142 -
obs--100 %

+
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://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