4LIQ: Extracellular domain of human CSF-1 receptor

Structure of the extracellular domain of human CSF-1 receptor in complex with the Fab fragment of RG7155. Determined by X-ray diffraction at 2.6 Å resolution. Released 18 Jun 2014.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 7,268
Mol. weight: 109.82 kDa
Ligands: NAG
Released: 18 Jun 2014

Explore 4LIQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LIQ contains 22 α-helices and 86 β-strands across 3 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 E: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	1
β-strand	29-32	4	2
β-strand	38-43	6	1
β-strand	49-51	3	2
β-strand	59-62	4	1
β-strand	66-71	6	1
α-helix	76-78	3
β-strand	80-85	6	2
β-strand	95-101	7	2
β-strand	108-110	3	3
β-strand	114-118	5	4
β-strand	123-125	3	5
β-strand	127-129	3	3
α-helix	132-137	6
β-strand	139-142	4	4
β-strand	154-157	4	5
β-strand	161-164	4	5
α-helix	169-171	3
β-strand	174-181	8	4
β-strand	184-187	4	4
β-strand	191-196	6	4
α-helix	203	1
β-strand	204-208	5	6
β-strand	211-215	5	7
β-strand	220-228	9	6
β-strand	234-239	6	7
β-strand	242-243	2	7
α-helix	246-247	2
β-strand	248-252	5	6
β-strand	257-265	9	6
β-strand	274-282	9	7
β-strand	285-296	12	7
β-strand	300-304	5	8
β-strand	310-314	5	9
β-strand	319-328	10	8
β-strand	333-338	6	9
α-helix	345-347	3
β-strand	351-354	4	8
β-strand	361-368	8	8
α-helix	373-375	3
β-strand	377-385	9	9
β-strand	388-399	12	9
β-strand	400-411	12	10
β-strand	414-424	11	10
α-helix	426-427	2
β-strand	428-435	8	11
β-strand	446-452	7	11
β-strand	456-459	4	10
β-strand	466-473	8	10
β-strand	481-488	8	11
β-strand	493-498	6	11

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	57-59	3	13
α-helix	61-63	3
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	87-89	3
β-strand	91-98	8	13
β-strand	103-106	4	13
β-strand	110-114	5	13
β-strand	120	1	14
β-strand	123-127	5	15
β-strand	138-148	11	15
β-strand	149	1	14
β-strand	154-157	4	16
α-helix	158-160	3
β-strand	162	1	16
β-strand	166-168	3	15
α-helix	169-171	3
β-strand	172-173	2	15
β-strand	179-188	10	15
α-helix	189-193	5
β-strand	198-203	6	16
α-helix	204-206	3
β-strand	208-213	6	16

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	85-90	6	18
β-strand	96-97	2	18
β-strand	101-105	5	18
β-strand	110	1	19
β-strand	113-117	5	20
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	20
β-strand	139	1	19
β-strand	143-149	7	21
β-strand	152-153	2	21
β-strand	158-162	5	20
α-helix	163-166	4
β-strand	172-181	10	20
α-helix	182-185	4
β-strand	190-197	8	21
β-strand	204-209	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Macrophage colony-stimulating factor 1 receptor	E	protein	553	Homo sapiens	P07333 (AlphaFold model)
Fab fragment RG7155 heavy chain	H	protein	223	Mus musculus
Fab fragment RG7155 light chain	L	protein	213	Mus musculus

Sequence of entity 1 (E), FASTA

>4LIQ_1 Macrophage colony-stimulating factor 1 receptor (chains E)
MGSGPGVLLLLLVATAWHGQGIPVIEPSVPELVVKPGATVTLRCVGNGSVEWDGPPSPHW
TLYSDGSSSILSTNNATFQNTGTYRCTEPGDPLGGSAAIHLYVKDPARPWNVLAQEVVVF
EDQDALLPCLLTDPVLEAGVSLVRVRGRPLMRHTNYSFSPWHGFTIHRAKFIQSQDYQCS
ALMGGRKVMSISIRLKVQKVIPGPPALTLVPAELVRIRGEAAQIVCSASSVDVNFDVFLQ
HNNTKLAIPQQSDFHNNRYQKVLTLNLDQVDFQHAGNYSCVASNVQGKHSTSMFFRVVES
AYLNLSSEQNLIQEVTVGEGLNLKVMVEAYPGLQGFNWTYLGPFSDHQPEPKLANATTKD
TYRHTFTLSLPRLKPSEAGRYSFLARNPGGWRALTFELTLRYPPEVSVIWTFINGSGTLL
CAASGYPQPNVTWLQCSGHTDRCDEAQVLQVWDDPYPEVLSQEPFHKVTVQSLLTVETLE
HNQTYECRAHNSVGSGSWAFIPISAGAHTHPPDEAAALEVLFQGPGTHHHHHHHHHHIGL
NDIFEAQKIEWHE

Sequence of entity 2 (H), FASTA

>4LIQ_2 Fab fragment RG7155 heavy chain (chains H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYDISWVRQAPGQGLEWMGVIWTDGGTNYA
QKLQGRVTMTTDTSTSTAYMELRSLRSDDTAVYYCARDQRLYFDVWGQGTTVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 3 (L), FASTA

>4LIQ_3 Fab fragment RG7155 light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASEDVNTYVSWYQQKPGKAPKLLIYAASNRYTGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSFSYPTFGQGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Water and common crystallization additives (SO4) are not listed.

Primary citation

Targeting tumor-associated macrophages with anti-CSF-1R antibody reveals a strategy for cancer therapy. Ries, C.H., Cannarile, M.A., Hoves, S. et al. Cancer Cell (2014) 25:846-859. DOI 10.1016/j.ccr.2014.05.016 · PubMed

Other PDB entries of the same protein (UniProt P07333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JOT 1.69 Å, Crystal structure of CSF-1R kinase domain with sulfatinib
6T2W 1.7 Å, Crystal structure of the CSF1R kinase domain with a dihydropurinone inhibitor (compound 4)
2I1M 1.8 Å, cFMS tyrosine kinase (tie2 KID) in complex with an arylamide inhibitor
6IG8 1.8 Å, Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952
2I0Y 1.9 Å, cFMS tyrosine kinase (FGF KID) in complex with an arylamide inhibitor
8CGC 1.93 Å, Structure of CSF1R in complex with a pyrollopyrimidine (compound 23)
3DPK 1.95 Å, cFMS tyrosine kinase in complex with a pyridopyrimidinone inhibitor
3BEA 2.02 Å, cFMS tyrosine kinase (tie2 KID) in complex with a pyrimidinopyridone inhibitor
3KRJ 2.1 Å, cFMS tyrosine kinase in complex with 4-Cyano-1H-imidazole-2-carboxylic acid…
6N33 2.25 Å, Crystal structure of fms kinase domain with a small molecular inhibitor, PLX5622
8W1L 2.26 Å, Structure of CSF1R kinase domain in complex with Cpd 32
3KRL 2.4 Å, cFMS Tyrosine kinase in complex with 5-Cyano-furan-2-carboxylic acid…

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