6UMX: Growth/differentiation factor 8

Structural basis for specific inhibition of extracellular activation of pro/latent myostatin by SRK-015. Determined by X-ray diffraction at 2.79 Å resolution. Released 26 Feb 2020.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,849
Mol. weight: 178.14 kDa
Released: 26 Feb 2020

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

Secondary structure: helices and β-sheets

6UMX contains 43 α-helices and 132 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: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	44-63	20
α-helix	74-80	7
α-helix	85-92	8
β-strand	114-120	7	1
α-helix	121-122	2
β-strand	123	1	2
β-strand	139	1	2
β-strand	151-160	10	1
α-helix	161-162	2
β-strand	167-175	9	3
β-strand	176	1	4
β-strand	186	1	4
β-strand	190-196	7	3
β-strand	202-207	6	1
α-helix	209-217	9
β-strand	225-230	6	3
β-strand	236	1	3
β-strand	252-257	6	1
β-strand	271	1	5
β-strand	283-284	2	5
β-strand	287-289	3	6
β-strand	298-300	3	7
β-strand	303-305	3	6
β-strand	308-309	2	5
β-strand	342-353	12	7
β-strand	358-372	15	7

Chain B: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	44-64	21
α-helix	74-80	7
α-helix	85-92	8
β-strand	114-120	7	7
α-helix	121-122	2
β-strand	123	1	31
β-strand	139	1	31
β-strand	151-160	10	7
α-helix	161-162	2
β-strand	163	1	32
β-strand	167-175	9	33
β-strand	176	1	34
β-strand	186	1	34
β-strand	190-196	7	33
β-strand	198	1	32
β-strand	202-207	6	7
α-helix	209-217	9
β-strand	225-230	6	33
β-strand	252-257	6	7
β-strand	271	1	35
β-strand	283-284	2	35
β-strand	287-289	3	36
β-strand	298-300	3	1
β-strand	303-305	3	36
β-strand	308-309	2	35
β-strand	340-353	14	1
β-strand	358-374	17	1

Chain h: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	10-12	3	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	32-39	8	27
β-strand	45-51	7	27
β-strand	58-60	3	27
α-helix	62-64	3
β-strand	68-73	6	26
α-helix	74-76	3
β-strand	78-83	6	26
α-helix	88-90	3
β-strand	92-102	11	27
α-helix	108-110	3
β-strand	120-124	5	27
β-strand	130	1	28
α-helix	131-132	2
β-strand	133-137	5	29
β-strand	148-158	11	29
β-strand	159	1	28
β-strand	164-167	4	30
α-helix	168-170	3
β-strand	176-178	3	29
α-helix	179-181	3
β-strand	182-183	2	29
β-strand	189-198	10	29
β-strand	207-213	7	30
α-helix	214-216	3
β-strand	218-224	7	30

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	10-12	3	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	32-39	8	16
β-strand	45-51	7	16
β-strand	58-60	3	16
α-helix	62-64	3
β-strand	68-73	6	15
α-helix	74-76	3
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-102	11	16
α-helix	108-110	3
β-strand	120-124	5	16
β-strand	130	1	17
α-helix	131-132	2
β-strand	133-137	5	18
β-strand	145	1	18
β-strand	148-158	11	18
β-strand	159	1	17
β-strand	164-167	4	19
α-helix	168-170	3
β-strand	176-178	3	18
α-helix	179-181	3
β-strand	182-183	2	18
β-strand	189-198	10	18
β-strand	207-213	7	19
α-helix	214-216	3
β-strand	218-224	7	19

Chain l: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	20
β-strand	5	1	21
β-strand	9-12	4	22
β-strand	18-23	6	21
α-helix	26-30	5
β-strand	35-39	5	22
β-strand	46-49	4	22
β-strand	50	1	23
β-strand	54	1	23
β-strand	63-68	6	21
β-strand	71-76	6	21
α-helix	81-83	3
β-strand	85-93	9	22
β-strand	97-100	4	22
β-strand	101	1	20
β-strand	104-108	5	22
β-strand	114	1	24
α-helix	115-116	2
β-strand	117-121	5	25
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-142	10	25
β-strand	143	1	24
β-strand	148-153	6	14
β-strand	156-158	3	14
β-strand	162-164	3	25
β-strand	168-169	2	25
β-strand	175-183	9	25
α-helix	185-189	5
β-strand	194-200	7	14
β-strand	203-209	7	14

Chain L: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	8
β-strand	5	1	9
β-strand	9-12	4	10
β-strand	18-23	6	9
α-helix	26-30	5
β-strand	35-39	5	10
β-strand	46-49	4	10
β-strand	50	1	11
β-strand	54	1	11
α-helix	55-56	2
β-strand	63-68	6	9
β-strand	71-76	6	9
α-helix	81-83	3
β-strand	85-93	9	10
β-strand	97-100	4	10
β-strand	101	1	8
β-strand	104-108	5	10
β-strand	114	1	12
α-helix	115-116	2
β-strand	117-121	5	13
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-142	10	13
β-strand	143	1	12
β-strand	148-153	6	14
β-strand	156-157	2	14
β-strand	162-164	3	13
β-strand	168-169	2	13
β-strand	175-183	9	13
α-helix	185-190	6
β-strand	194-200	7	14
β-strand	203-209	7	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Growth/differentiation factor 8	A, B	protein	365	Homo sapiens	O14793 (AlphaFold model)
GL29H4-16 Fab Light Chain,GL29H4-16 Fab Light Chain	L, l	protein	215	Homo sapiens	P0DOY2 (AlphaFold model)
GL29H4-16 Fab Heavy Chain,GL29H4-16 Fab Heavy Chain	H, h	protein	229	Homo sapiens	Q5EFE5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6UMX_1 Growth/differentiation factor 8 (chains A, B)
HHHHHHENLYFQSNENSEQKENVEKEGLCNACTWRQNTKSSRIEAIKIQILSKLRLETAP
NISKDVIRQLLPKAPPLRELIDQYDVQRADSSDGSLEDDDYHATTETIITMPTESDFLMQ
VDGKPKCCFFKFSSKIQYNKVVKAQLWIYLRPVETPTTVFVQILRLIKPMKDGTRYTGIR
SLKLDMNPGTGIWQSIDVKTVLQNWLKQPESNLGIEIKALDENGHDLAVTFPGPGEDGLN
PFLEVKVTDTPKASRADFGLDCDEHSTESRCCRYPLTVDFEAFGWDWIIAPKRYKANYCS
GECEFVFLQKYPHTHLVHQANPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVD
RCGCS

Sequence of entity 2 (L, l), FASTA

>6UMX_2 GL29H4-16 Fab Light Chain,GL29H4-16 Fab Light Chain (chains L, l)
QPVLTQPPSASGTPGQRVTISCSGSSSNIGSNPVHWYQQLPGTAPKLLIYDDNQRPSGVP
DRFSGSKSGTSASLVISGLQSDDEADYYCAAWDDSLNSVFGGGTKLTVLGQPKAAPSVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (H, h), FASTA

>6UMX_3 GL29H4-16 Fab Heavy Chain,GL29H4-16 Fab Heavy Chain (chains H, h)
QIQLVQSGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSRKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLLVRFLYWSHYYGMDVWGQGT
TVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Primary citation

Structural basis of specific inhibition of extracellular activation of pro- or latent myostatin by the monoclonal antibody SRK-015. Dagbay, K.B., Treece, E., Streich Jr., F.C. et al. J Biol Chem (2020) 295:5404-5418. DOI 10.1074/jbc.RA119.012293 · PubMed

Other PDB entries of the same protein (UniProt O14793 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5F3B 1.76 Å, Structure of myostatin in complex with chimeric RK35 antibody
5NTU 2.58 Å, Crystal Structure of human Pro-myostatin Precursor at 2.6 A Resolution
5F3H 2.7 Å, Structure of myostatin in complex with humanized RK35 antibody
5NXS 4.19 Å, Crystal Structure of Human Pro-myostatin Precursor at 4.2 A Resolution with Experimental…

Browse structure collections

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