9PVG: Co-crystal structure of two CCM2 PTB domains

Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3. Determined by X-ray diffraction at 3.0 Å resolution. Released 28 Jan 2026.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,573
Mol. weight: 84.8 kDa
Released: 28 Jan 2026

Explore 9PVG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PVG contains 16 α-helices and 36 β-strands across 6 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	63-76	14	1
β-strand	84	1	2
α-helix	85-97	13
α-helix	107-109	3
β-strand	110-115	6	1
β-strand	119-124	6	1
β-strand	130-135	6	1
α-helix	136-138	3
β-strand	139-147	9	1
β-strand	150-158	9	1
β-strand	193-200	8	1
α-helix	203-217	15

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	64-77	14	3
β-strand	84	1	4
α-helix	85-97	13
α-helix	107-109	3
β-strand	110-115	6	3
β-strand	119-124	6	3
β-strand	130-135	6	3
α-helix	136-138	3
β-strand	139-147	9	3
β-strand	150-158	9	3
β-strand	192-200	9	3
α-helix	203-216	14

Chains C and D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	63-76	14	5
α-helix	85-97	13
α-helix	107-109	3
β-strand	110-115	6	5
β-strand	119-124	6	5
β-strand	130-135	6	5
α-helix	136-138	3
β-strand	139-147	9	5
β-strand	150-158	9	5
β-strand	193-200	8	5
α-helix	203-219	17

Chains E and F: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	228-230	3	6
β-strand	243	1	2
β-strand	246-249	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Malcavernin	A, B, C, D	protein	180	Homo sapiens	Q9BSQ5 (AlphaFold model)
Krev interaction trapped protein 1	E, F	protein	29	Homo sapiens	O00522 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9PVG_1 Malcavernin (chains A, B, C, D)
GSERVEPDRLLSDYIEKEVKYLGQLTSIPGYLNPSSRTEILHFIDNAKRAHQLPGHLTQE
HDAVLSLSAYNVKLAWRDGEDIILRVPIHDIAAVSYVRDDAAHLVVLKTAQDPGISPSQS
LCAESSRGLSAGSLSESAVGPVEACCLVILAAESKVAAEELCCLLGQVFQVVYTESTIDF

Sequence of entity 2 (E, F), FASTA

>9PVG_2 Krev interaction trapped protein 1 (chains E, F)
TCIYNPLFGSDLQYTNRVDKVVINPYFGL

Primary citation

Dual recruitment of two CCM2 molecules to KRIT1 suppresses KLF4 expression. Huet-Calderwood, C., Fisher, O.S., Das, S. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-69595-7 · PubMed

Other PDB entries of the same protein (UniProt Q9BSQ5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4FQN 1.9 Å, Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD)
4YKD 1.93 Å, Crystal structure of truncated cerebral cavernous malformation 2 C-terminal adaptor domain
4YL6 2.1 Å, Crystal structure of truncated cerebral cavernous malformation 2 C-terminal adaptor…
4Y5O 2.35 Å, CCM2 HHD in complex with MEKK3 NPB1
4YKC 2.7 Å, Crystal structure of cerebral cavernous malformation 2 C-terminal adaptor domain
4WJ7 2.75 Å, CCM2 PTB domain in complex with KRIT1 NPxY/F3
4TVQ 2.8 Å, CCM3 in complex with CCM2 LD-like motif

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