[English] 日本語
Yorodumi
- PDB-7vup: Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin k... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vup
TitleStructure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment
Components
  • DNA (5'-D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3')
  • DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3')
  • Nuclear factor NF-kappa-B p52 subunit
KeywordsDNA BINDING PROTEIN/DNA / DNA-protein complex / transcription factor / TRANSCRIPTION / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / SUMOylation of immune response proteins / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation ...follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / SUMOylation of immune response proteins / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / canonical NF-kappaB signal transduction / spleen development / extracellular matrix organization / response to cytokine / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / TAK1-dependent IKK and NF-kappa-B activation / PKMTs methylate histone lysines / sequence-specific double-stranded DNA binding / rhythmic process / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor NF-kappa-B, p100 subunit / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. ...Nuclear factor NF-kappa-B, p100 subunit / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p100 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMeshcheryakov, V.A. / Wang, V.Y.-F.
Funding supportMacao, 2items
OrganizationGrant numberCountry
The Science and Technology Development Fund, Macao S.A.R. (FDCT)0104/2019/A2Macao
University of MacauMYRG2018-00093-FHSMacao
CitationJournal: Elife / Year: 2023
Title: Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation.
Authors: Pan, W. / Meshcheryakov, V.A. / Li, T. / Wang, Y. / Ghosh, G. / Wang, V.Y.
History
DepositionNov 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear factor NF-kappa-B p52 subunit
C: DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3')
B: Nuclear factor NF-kappa-B p52 subunit
D: DNA (5'-D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)98,5004
Polymers98,5004
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-36 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.987, 84.289, 140.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 34 - 329 / Label seq-ID: 34 - 329

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BC

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Nuclear factor NF-kappa-B p52 subunit


Mass: 43732.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB2, LYT10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q00653
#2: DNA chain DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3')


Mass: 5437.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3')


Mass: 5597.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium malonate, pH 4.0, 50mM CsCl, 2.5% PEG 3350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.4→46.85 Å / Num. obs: 14272 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.998 / Net I/σ(I): 9.6
Reflection shellResolution: 3.4→3.58 Å / Num. unique obs: 2025 / CC1/2: 0.782

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a3q

1a3q


Resolution: 3.4→45.451 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.922 / SU B: 58.887 / SU ML: 0.788 / Cross valid method: FREE R-VALUE / ESU R Free: 0.622
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2858 690 4.848 %
Rwork0.2712 13543 -
all0.272 --
obs-14233 99.699 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 156.456 Å2
Baniso -1Baniso -2Baniso -3
1-15.984 Å20 Å2-0 Å2
2--2.19 Å2-0 Å2
3----18.174 Å2
Refinement stepCycle: LAST / Resolution: 3.4→45.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 691 0 0 5359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135544
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154966
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0940.016497
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6687617
X-RAY DIFFRACTIONr_angle_other_deg1.3281.58611510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7225590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.0221.328256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32515870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4841540
X-RAY DIFFRACTIONr_chiral_restr0.1150.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021208
X-RAY DIFFRACTIONr_nbd_refined0.2050.2988
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.24845
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22481
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.23066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3240.218
X-RAY DIFFRACTIONr_nbd_other0.3050.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.7060.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.5090.21
X-RAY DIFFRACTIONr_mcbond_it10.76216.1552366
X-RAY DIFFRACTIONr_mcbond_other10.76416.1542365
X-RAY DIFFRACTIONr_mcangle_it17.23124.2362954
X-RAY DIFFRACTIONr_mcangle_other17.22924.2382955
X-RAY DIFFRACTIONr_scbond_it9.38116.9743178
X-RAY DIFFRACTIONr_scbond_other9.38116.9743178
X-RAY DIFFRACTIONr_scangle_it15.36125.2334663
X-RAY DIFFRACTIONr_scangle_other15.35925.2344664
X-RAY DIFFRACTIONr_lrange_it25.429307.46421777
X-RAY DIFFRACTIONr_lrange_other25.428307.45621778
X-RAY DIFFRACTIONr_ncsr_local_group_10.1190.058790
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.118570.0501
12BX-RAY DIFFRACTIONLocal ncs0.118570.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.7230.4791670.4813165X-RAY DIFFRACTION99.7008
3.723-4.160.311350.3362851X-RAY DIFFRACTION99.5002
4.16-4.7980.2431230.2082567X-RAY DIFFRACTION99.8145
4.798-5.8620.2251170.1972192X-RAY DIFFRACTION99.8271
5.862-8.2340.272950.2091727X-RAY DIFFRACTION100
8.234-45.4510.282530.291041X-RAY DIFFRACTION99.8175

+
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