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- PDB-8tqd: NF-Kappa-B1 Bound with a Covalent Inhibitor -

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Basic information

Entry
Database: PDB / ID: 8tqd
TitleNF-Kappa-B1 Bound with a Covalent Inhibitor
ComponentsNuclear factor NF-kappa-B p105 subunit
KeywordsTRANSCRIPTION / Transcription factor / DNA binding protein
Function / homology
Function and homology information


negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex ...negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / cellular response to dsRNA / Interleukin-1 processing / cellular response to interleukin-6 / actinin binding / cellular response to angiotensin / Regulation of NFE2L2 gene expression / negative regulation of protein metabolic process / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / positive regulation of transcription initiation by RNA polymerase II / canonical NF-kappaB signal transduction / cellular response to interleukin-1 / Purinergic signaling in leishmaniasis infection / JNK cascade / response to muscle stretch / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / response to cytokine / Activation of NF-kappaB in B cells / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / CLEC7A (Dectin-1) signaling / PKMTs methylate histone lysines / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Interleukin-1 signaling / HCMV Early Events / cellular response to mechanical stimulus / cellular response to nicotine / specific granule lumen / positive regulation of canonical Wnt signaling pathway / SARS-CoV-1 activates/modulates innate immune responses / Downstream TCR signaling / cellular response to tumor necrosis factor / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / secretory granule lumen / cellular response to lipopolysaccharide / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / apoptotic process / chromatin binding / chromatin / Neutrophil degranulation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Nuclear factor NF-kappa-B, p105 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 ...: / Nuclear factor NF-kappa-B, p105 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 repeat / 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
: / Nuclear factor NF-kappa-B p105 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsHilbert, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Cell / Year: 2024
Title: DrugMap: A quantitative pan-cancer analysis of cysteine ligandability.
Authors: Takahashi, M. / Chong, H.B. / Zhang, S. / Yang, T.Y. / Lazarov, M.J. / Harry, S. / Maynard, M. / Hilbert, B. / White, R.D. / Murrey, H.E. / Tsou, C.C. / Vordermark, K. / Assaad, J. / Gohar, ...Authors: Takahashi, M. / Chong, H.B. / Zhang, S. / Yang, T.Y. / Lazarov, M.J. / Harry, S. / Maynard, M. / Hilbert, B. / White, R.D. / Murrey, H.E. / Tsou, C.C. / Vordermark, K. / Assaad, J. / Gohar, M. / Durr, B.R. / Richter, M. / Patel, H. / Kryukov, G. / Brooijmans, N. / Alghali, A.S.O. / Rubio, K. / Villanueva, A. / Zhang, J. / Ge, M. / Makram, F. / Griesshaber, H. / Harrison, D. / Koglin, A.S. / Ojeda, S. / Karakyriakou, B. / Healy, A. / Popoola, G. / Rachmin, I. / Khandelwal, N. / Neil, J.R. / Tien, P.C. / Chen, N. / Hosp, T. / van den Ouweland, S. / Hara, T. / Bussema, L. / Dong, R. / Shi, L. / Rasmussen, M.Q. / Domingues, A.C. / Lawless, A. / Fang, J. / Yoda, S. / Nguyen, L.P. / Reeves, S.M. / Wakefield, F.N. / Acker, A. / Clark, S.E. / Dubash, T. / Kastanos, J. / Oh, E. / Fisher, D.E. / Maheswaran, S. / Haber, D.A. / Boland, G.M. / Sade-Feldman, M. / Jenkins, R.W. / Hata, A.N. / Bardeesy, N.M. / Suva, M.L. / Martin, B.R. / Liau, B.B. / Ott, C.J. / Rivera, M.N. / Lawrence, M.S. / Bar-Peled, L.
History
DepositionAug 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear factor NF-kappa-B p105 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1192
Polymers22,7381
Non-polymers3811
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.210, 57.210, 71.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Nuclear factor NF-kappa-B p105 subunit


Mass: 22738.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19838
#2: Chemical ChemComp-JMR / 1-(2-bromo-4-chlorophenyl)-N-{(3S)-1-[(E)-iminomethyl]pyrrolidin-3-yl}methanesulfonamide


Mass: 380.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15BrClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Citrate pH5.0, 20%w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→49.55 Å / Num. obs: 17269 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Rrim(I) all: 0.079 / Χ2: 0.99 / Net I/σ(I): 17.1 / Num. measured all: 182077
Reflection shellResolution: 2.02→2.07 Å / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 1.06 / Num. measured all: 13161 / Num. unique obs: 1278 / CC1/2: 0.679 / Rpim(I) all: 0.346 / Rrim(I) all: 1.116 / Χ2: 0.89 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→49.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.272 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22665 802 4.6 %RANDOM
Rwork0.18164 ---
obs0.1837 16462 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.667 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.06 Å2
Refinement stepCycle: 1 / Resolution: 2.02→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 20 99 1676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121649
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161593
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.7032232
X-RAY DIFFRACTIONr_angle_other_deg0.4131.6073675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4475202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.799511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1610289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
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_it2.5784.689808
X-RAY DIFFRACTIONr_mcbond_other2.5784.689808
X-RAY DIFFRACTIONr_mcangle_it3.9268.4251010
X-RAY DIFFRACTIONr_mcangle_other3.9258.4261011
X-RAY DIFFRACTIONr_scbond_it2.6845.118841
X-RAY DIFFRACTIONr_scbond_other2.6835.119842
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5089.2571223
X-RAY DIFFRACTIONr_long_range_B_refined7.19249.621803
X-RAY DIFFRACTIONr_long_range_B_other7.17549.361784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.746 63 -
Rwork0.431 1206 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 12.9663 Å / Origin y: 6.755 Å / Origin z: -0.7372 Å
111213212223313233
T0.0122 Å2-0.0202 Å2-0.0046 Å2-0.0469 Å20.0122 Å2--0.0096 Å2
L0.2617 °2-0.0632 °20.0546 °2-0.279 °2-0.103 °2--0.5093 °2
S-0.0266 Å °-0.0083 Å °-0.0017 Å °0.0024 Å °0.0008 Å °-0.0408 Å °-0.0375 Å °0.0605 Å °0.0259 Å °

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