7CLI: NF-kB p52 homodimer

Structure of NF-kB p52 homodimer bound to P-Selectin kB DNA fragment. Determined by X-ray diffraction at 3.0 Å resolution. Released 21 Jul 2021.

Method
X-ray diffraction
Resolution
3.0 Å
Organism
Homo sapiens
Chains
4
Atoms
5,359
Mol. weight
98.5 kDa
Released
21 Jul 2021

Explore 7CLI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CLI contains 28 α-helices and 60 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 30 β-strands

ElementResiduesLengthSheet
β-strand39-4461
α-helix451
β-strand4612
α-helix471
β-strand49-5133
α-helix52-532
β-strand5414
β-strand6712
β-strand79-8351
β-strand89-9685
β-strand10415
β-strand108-11034
β-strand120-12455
β-strand130-13231
β-strand137-13934
α-helix140-1423
α-helix143-16018
α-helix168-1703
α-helix171-18414
β-strand189-19023
β-strand191-19885
β-strand207-20825
α-helix209-2113
β-strand212-21325
α-helix214-2163
β-strand217-21933
α-helix227-2282
β-strand230-23346
β-strand237-23937
β-strand245-25066
β-strand260-26348
β-strand271-27338
β-strand27516
α-helix278-2803
β-strand28116
β-strand286-29056
α-helix291-2944
β-strand305-30958
β-strand31019
α-helix3161
β-strand31719
α-helix318-3203
β-strand321-32338
β-strand324-32637
α-helix327-3282
Chain B: 13 helices, 30 β-strands
ElementResiduesLengthSheet
β-strand39-44610
α-helix451
β-strand46111
α-helix471
α-helix51-533
β-strand54112
β-strand67111
β-strand79-83510
β-strand89-96813
β-strand104113
β-strand108-110312
β-strand114113
β-strand120-124513
β-strand130-132310
β-strand137-139312
α-helix140-1423
α-helix146-15510
α-helix168-17912
β-strand189-190214
β-strand191-198813
β-strand207-208213
α-helix209-2113
β-strand212-213213
α-helix214-2163
β-strand217-218214
α-helix226-2283
β-strand230-233415
β-strand239116
β-strand245-250615
β-strand260-264517
β-strand270-273417
β-strand275115
α-helix278-2803
β-strand281-282215
β-strand286-290515
α-helix291-2944
α-helix3021
β-strand303-309717
β-strand310118
β-strand317118
β-strand321-325517
β-strand326116
α-helix327-3282

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Nuclear factor NF-kappa-B p52 subunitA, Bprotein398Homo sapiensQ00653 (AlphaFold model)
DNA (5'-d(*cp*ap*ap*gp*gp*gp*gp*tp*cp*ap*cp*cp*cp*cp*cp*tp*tp*c)-3')CDNA18Homo sapiens
DNA (5'-d(*gp*ap*ap*gp*gp*gp*gp*gp*tp*gp*ap*cp*cp*cp*cp*tp*tp*g)-3')DDNA18Homo sapiens
Sequence of entity 1 (A, B), FASTA
>7CLI_1 Nuclear factor NF-kappa-B p52 subunit (chains A, B)
MESCYNPGLDGIIEYDDFKLNSSIVEPKEPAPETADGPYLVIVEQPKQRGFRFRYGCEGP
SHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLVTHSDPPRAHAHSLVGKQCSELGIC
AVSVGPKDMTAQFNNLGVLHVTKKNMMGTMIQKLQRQRLRSRPQGLTEAEQRELEQEAKE
LKKVMDLSIVRLRFSAFLRASDGSFSLPLKPVISQPIHDSKSPGASNLKISRMDKTAGSV
RGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIE
RPVTVFLQLKRKRGGDVSDSKQFTYYPLVEDKEEVQRKRRKALPTFSQPFGGGSHMGGGS
GGAAGGYGGAGGGGSLGFFPSSLAYSPYQSGAGPMGCY
Sequence of entity 2 (C), FASTA
>7CLI_2 DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*TP*CP*AP*CP*CP*CP*CP*CP*TP*TP*C)-3') (chains C)
CAAGGGGTCACCCCCTTC
Sequence of entity 3 (D), FASTA
>7CLI_3 DNA (5'-D(*GP*AP*AP*GP*GP*GP*GP*GP*TP*GP*AP*CP*CP*CP*CP*TP*TP*G)-3') (chains D)
GAAGGGGGTGACCCCTTG

Primary citation

Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. Pan, W., Meshcheryakov, V.A., Li, T. et al. Elife (2023) 12. DOI 10.7554/eLife.86258 · PubMed

Other PDB entries of the same protein (UniProt Q00653 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 7CLI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.