6VGD: PDB entry 6VGD

Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC. Determined by X-ray diffraction at 4.2 Å resolution. Released 25 Nov 2020.

Method
X-ray diffraction
Resolution
4.2 Å
Organism
Homo sapiens
Chains
5
Atoms
3,359
Mol. weight
59.7 kDa
Released
25 Nov 2020

Explore 6VGD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VGD contains 8 α-helices and 26 β-strands across 3 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: 4 helices, 4 β-strands

ElementResiduesLengthSheet
α-helix284-2874
α-helix294-2963
β-strand300-30231
β-strand309-31131
α-helix314-32512
α-helix332-34514
β-strand348-35031
β-strand358-36031
Chain D: 0 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand113-11422
β-strand121-12442
β-strand129-13133
β-strand140-14452
β-strand153-15754
β-strand168-16925
β-strand172-17434
β-strand179-18242
β-strand186-18725
β-strand200-20454
β-strand209-21024
β-strand218-22033
Chain G: 4 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix8-125
α-helix16-194
β-strand25-2956
α-helix37-5014
β-strand52-5766
β-strand62-6766
β-strand94-9526
β-strand102-10324
β-strand106-10724
β-strand10817
β-strand114-11526
β-strand120-12346
β-strand12717
α-helix129-1379

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Friend leukemia integration 1 transcription factorAprotein104Homo sapiensQ01543 (AlphaFold model)
DNA (5'-d(p*cp*ap*gp*ap*gp*gp*ap*tp*gp*tp*gp*gp*cp*tp*tp*c)-3')BDNA16Homo sapiens
DNA (5'-d(p*gp*ap*ap*gp*cp*cp*ap*cp*ap*tp*cp*cp*tp*cp*tp*g)-3')CDNA16Homo sapiens
Runt-related transcription factor 2Dprotein177Homo sapiensQ13950 (AlphaFold model)
Core-binding factor subunit betaGprotein156Homo sapiensQ13951 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6VGD_1 Friend leukemia integration 1 transcription factor (chains A)
GPHMPGSGQIQLWQFLLELLSDSANASCITWEGTNGEFKMTDPDEVARRWGERKSKPNMN
YDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPTE
Sequence of entity 2 (B), FASTA
>6VGD_2 DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') (chains B)
CAGAGGATGTGGCTTC
Sequence of entity 3 (C), FASTA
>6VGD_3 DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3') (chains C)
GAAGCCACATCCTCTG
Sequence of entity 4 (D), FASTA
>6VGD_4 Runt-related transcription factor 2 (chains D)
AELVRTDSPNFLCSVLPSHWRCNKTLPVAFKVVALGEVPDGTVVTVMAGNDENYSAELRN
ASAVMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKVTVDGPREPRRH
RQKLDDSKPSLFSDRLSDLGRIPHPSMRVGVPPQNPRPSLNSAPSPFNPQGQSQITD
Sequence of entity 5 (G), FASTA
>6VGD_5 Core-binding factor subunit beta (chains G)
MGSSHHHHHHSQDPMPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQN
ACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGV
CVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQA

Primary citation

Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins. Hou, C., Mandal, A., Rohr, J. et al. Structure (2021) 29:404-412.e4. DOI 10.1016/j.str.2020.11.012 · PubMed

Other PDB entries of the same protein (UniProt Q01543 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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