3QBV: Cell division control protein 42 homolog

Structure of designed orthogonal interaction between CDC42 and nucleotide exchange domains of intersectin. Determined by X-ray diffraction at 2.65 Å resolution. Released 8 Feb 2012.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,068
Mol. weight: 121.93 kDa
Ligands: GDP
Released: 8 Feb 2012

Explore 3QBV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QBV contains 49 α-helices and 31 β-strands across 4 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
α-helix	16-24	9
β-strand	41-46	6	1
β-strand	49-57	9	1
α-helix	68-71	4
β-strand	77-83	7	1
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	1
α-helix	117-119	3
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	1
α-helix	165-177	13

Chain B: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1233-1259	27
α-helix	1260-1264	5
α-helix	1265-1269	5
α-helix	1275-1282	8
α-helix	1285-1306	22
α-helix	1316-1322	7
α-helix	1323-1325	3
α-helix	1328-1349	22
α-helix	1351-1360	10
α-helix	1364-1366	3
α-helix	1371-1374	4
α-helix	1377-1394	18
α-helix	1403-1439	37
β-strand	1440	1	2
β-strand	1454	1	3
β-strand	1460	1	3
β-strand	1463-1467	5	4
β-strand	1479-1483	5	4
β-strand	1487-1490	4	4
β-strand	1492-1493	2	2
β-strand	1511-1512	2	2
β-strand	1525-1527	3	5
β-strand	1540-1542	3	5
β-strand	1547-1548	2	5
α-helix	1562-1575	14

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	16-24	9
β-strand	41-46	6	6
β-strand	49-57	9	6
α-helix	68-71	4
β-strand	77-83	7	6
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	6
α-helix	117-119	3
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	6
α-helix	165-177	13

Chain D: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1233-1259	27
α-helix	1260-1264	5
α-helix	1265-1269	5
α-helix	1275-1282	8
α-helix	1285-1306	22
α-helix	1316-1322	7
α-helix	1323-1325	3
α-helix	1328-1349	22
α-helix	1351-1360	10
α-helix	1364-1366	3
α-helix	1371-1374	4
α-helix	1377-1394	18
α-helix	1403-1439	37
β-strand	1440-1441	2	7
β-strand	1454	1	8
β-strand	1460	1	8
β-strand	1463-1467	5	9
β-strand	1480-1483	4	9
β-strand	1487-1489	3	9
β-strand	1490-1491	2	7
β-strand	1512-1514	3	7
α-helix	1563-1575	13
α-helix	1576-1578	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell division control protein 42 homolog	A, C	protein	178	Homo sapiens	P60953 (AlphaFold model)
Intersectin-1	B, D	protein	351	Homo sapiens	Q15811 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3QBV_1 Cell division control protein 42 homolog (chains A, C)
MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLRDTAG
QEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLR
DDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALE

Sequence of entity 2 (B, D), FASTA

>3QBV_2 Intersectin-1 (chains B, D)
DMLTPTERKRQGYIHELIVTEENYVNDLQLVTEIFQKPLMESELLTEKEVAMIFVNWKEL
IMCNIKLLKALRVRKKMSGEKMPVKMIGDILSAQLPHMQPYIRFCSRQLNGAALIQQKTD
EAPDFKEFVKRLAMDPRCKGMPLSEFILKPMQRVTRYPLIIKNILENTPENHPDHSHLKH
ALEKAEELCSQVNEGVREKENSDRLEWIQAHVQCEGLSEQLVFNSVTNCLGPRKFLHSGK
LYKAKSNKELYGFLFNDFLLLTQITKPLGSSGTDKVFSPKSNLQYKMYKTPIFLNEVLVK
LPTDPSGDEPIFHISHIDRVYTLRAESINERTAWVQKIKAASELYIETEKK

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Kapp, G.T., Liu, S., Stein, A. et al. Proc Natl Acad Sci U S A (2012) 109:5277-5282. DOI 10.1073/pnas.1114487109 · PubMed

Other PDB entries of the same protein (UniProt P60953 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2NGR 1.9 Å, Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution…
4JS0 1.9 Å, Complex of Cdc42 with the CRIB-PR domain of IRSp53
6SUP 2.0 Å, Crystal Structure of TcdB2-TccC3-Cdc42
3VHL 2.08 Å, Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)
1GRN 2.1 Å, Crystal structure of the CDC42/CDC42GAP/ALF3 complex.
1NF3 2.1 Å, Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity…
2DFK 2.15 Å, Crystal structure of the CDC42-Collybistin II complex
2WM9 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
2WMO 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
1GZS 2.3 Å, Crystal structure of the complex between the gef domain of the salmonella typhimurium…
1KI1 2.3 Å, Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42
3GCG 2.3 Å, crystal structure of MAP and CDC42 complex

Browse structure collections

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