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- PDB-3gut: Crystal structure of a higher-order complex of p50:RelA bound to ... -

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Basic information

Entry
Database: PDB / ID: 3gut
TitleCrystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR
Components
  • HIV-LTR Core Forward Strand
  • HIV-LTR Core Reverse Strand
  • Nuclear factor NF-kappa-B p105 subunit
  • Transcription factor p65
KeywordsTRANSCRIPTION/DNA / IG Fold / Protein-DNA Complex / Pseudocontinuous Helix / Rel Family / Multiprotein Assembly / Acetylation / Activator / Alternative splicing / Cytoplasm / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / ANK repeat / Apoptosis / Polymorphism / S-nitrosylation / TRANSCRIPTION-DNA COMPLEX
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 / acetaldehyde metabolic process / cellular response to interleukin-17 / prolactin signaling pathway ...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 / acetaldehyde metabolic process / cellular response to interleukin-17 / prolactin signaling pathway / 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 Schwann cell differentiation / positive regulation of lipid storage / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / negative regulation of interleukin-12 production / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / SUMOylation of immune response proteins / negative regulation of protein sumoylation / cellular response to dsRNA / nucleotide-binding oligomerization domain containing 2 signaling pathway / postsynapse to nucleus signaling pathway / defense response to tumor cell / Interleukin-1 processing / cellular response to interleukin-6 / actinin binding / negative regulation of protein metabolic process / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / cellular response to lipoteichoic acid / response to muramyl dipeptide / The NLRP3 inflammasome / general transcription initiation factor binding / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / cellular response to interleukin-1 / cellular defense response / Purinergic signaling in leishmaniasis infection / JNK cascade / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / NF-kB is activated and signals survival / positive regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / response to interleukin-1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / negative regulation of angiogenesis / negative regulation of miRNA transcription / response to progesterone / liver development / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / Activation of NF-kappaB in B cells / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / animal organ morphogenesis / B cell receptor signaling pathway / protein catabolic process / TAK1-dependent IKK and NF-kappa-B activation / response to insulin / negative regulation of protein catabolic process / transcription coactivator binding / chromatin DNA binding / cellular response to hydrogen peroxide / PKMTs methylate histone lysines
Similarity search - Function
Rel homology domain (RHD), DNA-binding domain / : / Nuclear factor NF-kappa-B, p105 subunit / Transcription factor RelA (p65) / 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 domain (RHD), DNA-binding domain / : / Nuclear factor NF-kappa-B, p105 subunit / Transcription factor RelA (p65) / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsStroud, J.C. / Oltman, A.J. / Han, A. / Bates, D.L. / Chen, L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural basis of HIV-1 activation by NF-kappaB--a higher-order complex of p50:RelA bound to the HIV-1 LTR.
Authors: Stroud, J.C. / Oltman, A. / Han, A. / Bates, D.L. / Chen, L.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor p65
B: Nuclear factor NF-kappa-B p105 subunit
C: Transcription factor p65
D: Nuclear factor NF-kappa-B p105 subunit
E: Transcription factor p65
F: Nuclear factor NF-kappa-B p105 subunit
G: Transcription factor p65
H: Nuclear factor NF-kappa-B p105 subunit
X: HIV-LTR Core Forward Strand
Y: HIV-LTR Core Reverse Strand
I: HIV-LTR Core Forward Strand
J: HIV-LTR Core Reverse Strand


Theoretical massNumber of molelcules
Total (without water)295,59012
Polymers295,59012
Non-polymers00
Water0
1
A: Transcription factor p65
B: Nuclear factor NF-kappa-B p105 subunit
C: Transcription factor p65
D: Nuclear factor NF-kappa-B p105 subunit
X: HIV-LTR Core Forward Strand
Y: HIV-LTR Core Reverse Strand


Theoretical massNumber of molelcules
Total (without water)147,7956
Polymers147,7956
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-85.6 kcal/mol
Surface area61870 Å2
MethodPISA
2
E: Transcription factor p65
F: Nuclear factor NF-kappa-B p105 subunit
G: Transcription factor p65
H: Nuclear factor NF-kappa-B p105 subunit
I: HIV-LTR Core Forward Strand
J: HIV-LTR Core Reverse Strand


Theoretical massNumber of molelcules
Total (without water)147,7956
Polymers147,7956
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-81.9 kcal/mol
Surface area61830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.493, 167.493, 172.757
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
DetailsTHE BIOLOGICAL UNIT IS MADE BY CHAINS A,B,C,D,X,Y. A NCS-RELATED UNIT IS MADE BY CHAINS E,F,G,H,I,J. TWO BIOLOGICAL UNITS ARE PRESENT IN THE ASYMMETRIC UNIT.

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Components

#1: Protein
Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit


Mass: 30984.045 Da / Num. of mol.: 4 / Fragment: UNP residues 20-291 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q04206
#2: Protein
Nuclear factor NF-kappa-B p105 subunit / DNA-binding factor KBF1 / EBP-1 / Nuclear factor NF-kappa-B p50 subunit


Mass: 34924.871 Da / Num. of mol.: 4 / Fragment: UNP residues 41-352 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19838
#3: DNA chain HIV-LTR Core Forward Strand


Mass: 7995.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HIV-LTR Core Forward Strand / Source: (natural) Human immunodeficiency virus
#4: DNA chain HIV-LTR Core Reverse Strand


Mass: 7982.157 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HIV-LTR Core Reverse Strand / Source: (natural) Human immunodeficiency virus
Sequence detailsACCORDING TO AUTHORS, THE CORRECT SEQUENCE OF ENTITY 1 (CHAINS A,C,E,G) IS NCBI LOCUS NP_033071, ...ACCORDING TO AUTHORS, THE CORRECT SEQUENCE OF ENTITY 1 (CHAINS A,C,E,G) IS NCBI LOCUS NP_033071, RESIDUES 20 TO 291, AS SHOWN IN THE COORDINATES. THE EXTRA RESIDUE NUMBER 19 IS A CLONING ARTIFACT. FOR ENTITY 2 (CHAINS B,D,F,H), THE CORRECT SEQUENCE IS THE NCBI LOCUS NP_032715, RESIDUES 39 TO 350. THE DIFFERENCE IN RESIDUE NUMBERING COMES FROM THE UNIPROT/SWISSPROT NUMBERING SCHEME. THIS SEEMS TO BE THE TRADITIONAL NUMBERING SCHEME FOR THIS FAMILY OF PROTEINS.

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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: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 50mM BTP pH 6.3, 50mM CaCl2, 7% w/v PEG 3000, 1mM Spermine, 10mM DTT, 8% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1BTP11
2CaCl211
3PEG 300011
4Spermine11
5DTT11
6Glycerol11
7BTP12
8CaCl212
9PEG 300012
10Spermine12
11DTT12
12Glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0688 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2003
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0688 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 47283 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.076 / Χ2: 1.005 / Net I/σ(I): 23.101
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.5-3.645.50.84845761.44696.5
3.94-4.096.60.64447411.128100
4.09-4.286.90.36246831.023100
4.28-4.57.20.2447381.01100
4.5-4.797.60.16947260.948100
4.79-5.167.80.12347480.922100
5.16-5.677.80.0947520.897100
5.67-6.497.80.07347440.895100
6.49-8.187.70.04747650.928100
8.18-507.50.0348101.0399.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VKX

1vkx


Resolution: 3.59→46.45 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: 60.1506 / σ(F): 6020
Details: Authors state that the differences between sfcheck parameters and the CNS calculated values are due to the bulk solvent correction parameters used in refinement
RfactorNum. reflection% reflection
Rfree0.301 4541 8.2 %
Rwork0.245 --
obs-45190 81.2 %
Solvent computationBsol: 57.854 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso max: 200 Å2 / Biso mean: 150.501 Å2 / Biso min: 32.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.977 Å20 Å20 Å2
2---2.977 Å20 Å2
3---5.954 Å2
Refinement stepCycle: LAST / Resolution: 3.59→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18520 2120 0 0 20640
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it8.0611.5
X-RAY DIFFRACTIONc_scbond_it11.9772
X-RAY DIFFRACTIONc_mcangle_it12.7622
X-RAY DIFFRACTIONc_scangle_it16.5992.5
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used
3.59-3.610.386788X-RAY DIFFRACTION50
3.61-3.640.3809730X-RAY DIFFRACTION50
3.64-3.660.4195843X-RAY DIFFRACTION50
3.66-3.690.4383920X-RAY DIFFRACTION50
3.69-3.720.3674730X-RAY DIFFRACTION50
3.72-3.750.3575846X-RAY DIFFRACTION50
3.75-3.780.3441849X-RAY DIFFRACTION50
3.78-3.80.3516877X-RAY DIFFRACTION50
3.8-3.840.3751805X-RAY DIFFRACTION50
3.84-3.870.3717687X-RAY DIFFRACTION50
3.87-3.90.3682915X-RAY DIFFRACTION50
3.9-3.930.3208809X-RAY DIFFRACTION50
3.93-3.970.3474772X-RAY DIFFRACTION50
3.97-4.010.2926890X-RAY DIFFRACTION50
4.01-4.040.3065871X-RAY DIFFRACTION50
4.04-4.080.3093900X-RAY DIFFRACTION50
4.08-4.120.313832X-RAY DIFFRACTION50
4.12-4.170.2794934X-RAY DIFFRACTION50
4.17-4.210.2887924X-RAY DIFFRACTION50
4.21-4.260.2752896X-RAY DIFFRACTION50
4.26-4.30.3019962X-RAY DIFFRACTION50
4.3-4.350.2721943X-RAY DIFFRACTION50
4.35-4.410.2715935X-RAY DIFFRACTION50
4.41-4.460.2516947X-RAY DIFFRACTION50
4.46-4.520.2443921X-RAY DIFFRACTION50
4.52-4.580.2308961X-RAY DIFFRACTION50
4.58-4.650.2406961X-RAY DIFFRACTION50
4.65-4.720.2441944X-RAY DIFFRACTION50
4.72-4.790.2394969X-RAY DIFFRACTION50
4.79-4.870.258940X-RAY DIFFRACTION50
4.87-4.960.2561948X-RAY DIFFRACTION50
4.96-5.050.2436988X-RAY DIFFRACTION50
5.05-5.140.2599957X-RAY DIFFRACTION50
5.14-5.250.2256969X-RAY DIFFRACTION50
5.25-5.360.2273989X-RAY DIFFRACTION50
5.36-5.490.2207976X-RAY DIFFRACTION50
5.49-5.620.2244996X-RAY DIFFRACTION50
5.62-5.770.203949X-RAY DIFFRACTION50
5.77-5.940.203980X-RAY DIFFRACTION50
5.94-6.140.22851001X-RAY DIFFRACTION50
6.14-6.350.2271992X-RAY DIFFRACTION50
6.35-6.610.249970X-RAY DIFFRACTION50
6.61-6.910.2324988X-RAY DIFFRACTION50
6.91-7.270.2321995X-RAY DIFFRACTION50
7.27-7.720.2236985X-RAY DIFFRACTION50
7.72-8.320.211998X-RAY DIFFRACTION50
8.32-9.150.19811030X-RAY DIFFRACTION50
9.15-10.460.2334998X-RAY DIFFRACTION50
10.46-13.130.2319992X-RAY DIFFRACTION50
13.13-46.450.32481011X-RAY DIFFRACTION50
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna.param

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