1M63: PDB entry 1M63

Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Sept 2002.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: HOMO SAPIENS, TOLYPOCLADIUM INFLATUM
Chains: 8
Atoms: 11,185
Mol. weight: 163.21 kDa
Ligands: ZN, FE, CA
Released: 25 Sept 2002

Explore 1M63 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1M63 contains 60 α-helices and 76 β-strands across 8 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: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	22-25	4
β-strand	29	1	1
α-helix	31-34	4
β-strand	35	1	2
β-strand	41	1	2
α-helix	43-50	8
β-strand	56	1	1
α-helix	58-73	16
β-strand	78-81	4	3
β-strand	85-88	4	4
α-helix	95-104	10
β-strand	112-115	4	4
α-helix	126-139	14
β-strand	144-146	3	4
α-helix	154-159	6
α-helix	162-169	8
α-helix	172-183	12
β-strand	188-191	4	3
β-strand	195-197	3	3
α-helix	209-213	5
α-helix	226-232	7
β-strand	234-235	2	5
β-strand	248-250	3	5
β-strand	258-260	3	5
α-helix	262-271	10
β-strand	276-278	3	3
β-strand	293	1	6
β-strand	300	1	6
β-strand	302	1	3
α-helix	311-313	3
β-strand	319-325	7	4
β-strand	328-334	7	4
α-helix	344-346	3
α-helix	349-369	21

Chain B: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	16-29	14
β-strand	37	1	7
α-helix	54-61	8
β-strand	69	1	7
α-helix	71-78	8
β-strand	82	1	8
α-helix	87-98	12
β-strand	106	1	9
α-helix	108-118	11
α-helix	125-139	15
β-strand	147	1	9
α-helix	149-153	5
β-strand	167	1	8

Chain C: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	10
β-strand	15-24	10	10
α-helix	30-41	12
β-strand	52	1	10
β-strand	55-57	3	10
β-strand	61-64	4	10
β-strand	83	1	11
β-strand	97-100	4	10
β-strand	102	1	12
β-strand	108	1	11
β-strand	112-115	4	10
α-helix	120-122	3
β-strand	123	1	13
β-strand	126	1	13
β-strand	128-134	7	10
α-helix	136-143	8
β-strand	156-163	8	10

Chains D and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	5	1	12

Chain E: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	27-28	2
β-strand	29	1	14
α-helix	31-34	4
α-helix	43-51	9
β-strand	56	1	14
α-helix	58-73	16
β-strand	78-81	4	15
β-strand	85-90	6	16
α-helix	96-105	10
β-strand	113-117	5	16
α-helix	126-139	14
β-strand	144-146	3	16
α-helix	155-158	4
α-helix	162-169	8
α-helix	172-181	10
β-strand	188-191	4	15
β-strand	195-197	3	15
α-helix	210-213	4
α-helix	220-222	3
α-helix	226-232	7
β-strand	234-235	2	17
β-strand	248-250	3	17
β-strand	258-260	3	17
α-helix	262-265	4
α-helix	268-272	5
β-strand	276-279	4	15
β-strand	288-290	3	15
β-strand	293-294	2	18
β-strand	299-300	2	18
β-strand	302-305	4	15
α-helix	311-313	3
β-strand	319-325	7	16
β-strand	328-334	7	16
α-helix	344-346	3
α-helix	349-360	12
α-helix	362-365	4

Chain F: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	26-29	4
β-strand	36-37	2	19
α-helix	39-42	4
α-helix	46-48	3
α-helix	56-59	4
β-strand	69-70	2	19
α-helix	71-77	7
α-helix	78-81	4
α-helix	87-95	9
β-strand	106-107	2	20
α-helix	108-118	11
α-helix	125-137	13
β-strand	146-147	2	20
α-helix	149-156	8
α-helix	162-164	3

Chain G: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	21
β-strand	15-24	10	21
α-helix	30-41	12
β-strand	51-52	2	21
β-strand	55-56	2	21
β-strand	61-64	4	21
β-strand	66	1	21
β-strand	83	1	22
β-strand	97-100	4	21
β-strand	102	1	23
β-strand	108	1	22
β-strand	112-115	4	21
α-helix	120-122	3
β-strand	128-134	7	21
α-helix	136-143	8
β-strand	156-161	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine protein phosphatase 2B catalytic subunit, alpha isoform	A, E	protein	372	HOMO SAPIENS	Q08209 (AlphaFold model)
Calcineurin B subunit isoform 1	B, F	protein	169	HOMO SAPIENS	P63098 (AlphaFold model)
Peptidyl-prolyl cis-trans isomerase a	C, G	protein	165	HOMO SAPIENS	P62937 (AlphaFold model)
Cyclosporin a	D, H	protein	11	TOLYPOCLADIUM INFLATUM

Sequence of entity 1 (A, E), FASTA

>1M63_1 SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM (chains A, E)
MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESV
ALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYV
DRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMD
AFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFG
NEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFP
SLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEK
VTEMLVNVLNIC

Sequence of entity 2 (B, F), FASTA

>1M63_2 CALCINEURIN B SUBUNIT ISOFORM 1 (chains B, F)
GNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDI
FDTDGNGEVDFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVG
NNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLDIHKKMVVDV

Sequence of entity 3 (C, G), FASTA

>1M63_3 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A (chains C, G)
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGF
MCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTE
WLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

Sequence of entity 4 (D, H), FASTA

>1M63_4 CYCLOSPORIN A (chains D, H)
ALLVTAGLVLA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
FE	FE (III) ion	Fe	2
CA	Calcium ion	Ca	8

Primary citation

Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes. Huai, Q., Kim, H.-Y., Liu, Y. et al. Proc Natl Acad Sci U S A (2002) 99:12037. DOI 10.1073/PNAS.192206699 · PubMed

Other PDB entries of the same protein (UniProt Q08209 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2W73 1.45 Å, High-resolution structure of the complex between calmodulin and a peptide from…
4F0Z 1.7 Å, Crystal Structure of Calcineurin in Complex with the Calcineurin-Inhibiting Domain of…
6UUQ 1.85 Å, Structure of Calcineurin bound to RCAN1
2R28 1.86 Å, The complex Structure of Calmodulin Bound to a Calcineurin Peptide
6NUC 1.9 Å, Structure of Calcineurin in complex with NHE1 peptide
6NUF 1.9 Å, Structure of Calcineurin in complex with NHE1 peptide
4Q5U 1.95 Å, Structure of calmodulin bound to its recognition site from calcineurin
3LL8 2.0 Å, Crystal Structure of Calcineurin in Complex with AKAP79 Peptide
9NXE 2.09 Å, Crystal Structure of Calcineurin Clinical Variant E282K
1AUI 2.1 Å, Human calcineurin heterodimer
9NXN 2.1 Å, Crystal structure of CN:RII alpha
2P6B 2.3 Å, Crystal Structure of Human Calcineurin in Complex with PVIVIT Peptide

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