3MJG: Platelet derived growth factor receptor complex

The structure of a platelet derived growth factor receptor complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 16 Jun 2010.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,254
Mol. weight: 107.28 kDa
Ligands: NAG, NDG
Released: 16 Jun 2010

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

Secondary structure: helices and β-sheets

3MJG contains 10 α-helices and 72 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: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	1
α-helix	11	1
β-strand	13	1	2
β-strand	17-24	8	3
α-helix	27-29	3
β-strand	35	1	4
β-strand	38-40	3	5
β-strand	43-50	8	3
β-strand	58-78	21	5
β-strand	81-101	21	5

Chain B: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	5
β-strand	17-24	8	2
α-helix	27-30	4
β-strand	35	1	6
β-strand	37-40	4	1
β-strand	43-50	8	2
β-strand	58-78	21	1
β-strand	81-101	21	1

Chain X: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	7
β-strand	41-43	3	8
β-strand	50-56	7	7
β-strand	61-63	3	8
β-strand	64	1	9
β-strand	67	1	9
β-strand	71-75	5	7
β-strand	81-87	7	7
α-helix	92-94	3
β-strand	96-101	6	8
β-strand	114-119	6	8
β-strand	127	1	10
α-helix	128-129	2
α-helix	132-135	4
β-strand	136-139	4	11
β-strand	145-147	3	12
β-strand	151	1	10
β-strand	158-162	5	11
α-helix	168-169	2
β-strand	173-174	2	12
β-strand	178-181	4	12
β-strand	187-194	8	11
β-strand	197-200	4	11
β-strand	204-208	5	11
β-strand	217-220	4	13
β-strand	224-226	3	14
β-strand	231-238	8	13
β-strand	243	1	6
β-strand	244-248	5	15
β-strand	261-264	4	13
β-strand	271-278	8	13
β-strand	287-295	9	15
β-strand	300-308	9	15
β-strand	309-311	3	14

Chain Y: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	16
β-strand	41-43	3	17
β-strand	50-56	7	16
β-strand	62-63	2	18
β-strand	72-76	5	16
β-strand	80-87	8	16
α-helix	92-94	3
β-strand	96-98	3	17
β-strand	99-100	2	18
β-strand	116-119	4	17
α-helix	132-135	4
β-strand	136-139	4	19
β-strand	145-147	3	20
β-strand	159-162	4	19
α-helix	168-169	2
β-strand	173-174	2	20
β-strand	178-181	4	20
β-strand	187-194	8	19
β-strand	197-200	4	19
β-strand	204-208	5	19
β-strand	217-220	4	21
β-strand	224-226	3	22
β-strand	231-238	8	21
β-strand	243	1	4
β-strand	244-248	5	23
β-strand	261-264	4	21
β-strand	271-278	8	21
β-strand	287-294	8	23
β-strand	301-308	8	23
β-strand	309-311	3	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Platelet-derived growth factor subunit B	A, B	protein	172	Homo sapiens	P01127 (AlphaFold model)
Beta-type platelet-derived growth factor receptor	X, Y	protein	289	Homo sapiens	P09619 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3MJG_1 Platelet-derived growth factor subunit B (chains A, B)
EGDPIPEELYEMLSDHSIRSFDDLQRLLHGDPGEEDGAELDLNMTRSHSGGELESLARGR
RSLGSLTIAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQ
CRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAAHHHHHHH

Sequence of entity 2 (X, Y), FASTA

>3MJG_2 Beta-type platelet-derived growth factor receptor (chains X, Y)
LVVTPPGPELVLNVSSTFVLTCSGSAPVVWERMSQEPPQEMAKAQDGTFSSVLTLTNLTG
LDTGEYFCTHNDSRGLETDERKRLYIFVPDPTVGFLPNDAEELFIFLTEITEITIPCRVT
DPQLVVTLHEKKGDVALPVPYDHQRGFSGIFEDRSYICKTTIGDREVDSDAYYVYRLQVS
SINVSVNAVQTVVRQGENITLMCIVIGNEVVNFEWTYPRKESGRLVEPVTDFLLDMPYHI
RSILHIPSAELEDSGTYTCNVTESVNDHQDEKAINITVVESGHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	13
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	C8 H15 N O6	1

Primary citation

Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex. Shim, A.H., Liu, H., Focia, P.J. et al. Proc Natl Acad Sci U S A (2010) 107:11307-11312. DOI 10.1073/pnas.1000806107 · PubMed

Other PDB entries of the same protein (UniProt P01127 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HQU 2.2 Å, Crystal structure of human PDGF-BB in complex with a modified nucleotide aptamer…
4HQX 2.3 Å, CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer…
4QCI 2.3 Å, PDGF-B blocking antibody bound to PDGF-BB
6T9E 2.99 Å, Crystal structure of a bispecific DutaFab in complex with human PDGF
1PDG 3.0 Å, Crystal structure of human platelet-derived growth factor bb

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