1IM9: PDB entry 1IM9

Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1 bound to its MHC ligand HLA-Cw4. Determined by X-ray diffraction at 2.8 Å resolution. Released 30 May 2001.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 7
Atoms: 8,096
Mol. weight: 115.06 kDa
Released: 30 May 2001

Explore 1IM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1IM9 contains 30 α-helices and 84 β-strands across 5 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	225-227	3
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain D: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	8
β-strand	17-19	3	9
β-strand	24-30	7	8
β-strand	36-42	7	10
β-strand	47-52	6	10
β-strand	54-55	2	8
β-strand	60-66	7	8
α-helix	71-73	3
β-strand	75-82	8	10
α-helix	92	1
β-strand	93	1	10
α-helix	94-96	3
β-strand	97-99	3	10
β-strand	100-102	3	9
α-helix	106-108	3
β-strand	109-113	5	11
β-strand	117-118	2	12
β-strand	123-130	8	11
β-strand	136-141	6	13
β-strand	148-151	4	13
α-helix	152	1
β-strand	153-154	2	11
β-strand	160-168	9	11
β-strand	173-181	9	13
β-strand	184-188	5	13
α-helix	190-193	4
β-strand	195-197	3	13
β-strand	198-199	2	12

Chain E: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	14
α-helix	20	1
β-strand	21-28	8	14
β-strand	31-37	7	14
β-strand	46-47	2	14
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	14
β-strand	109-118	10	14
β-strand	121-125	5	14
β-strand	135	1	14
α-helix	139-148	10
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-179	15
β-strand	183	1	15
α-helix	184-185	2
β-strand	186-193	8	16
β-strand	198-208	11	16
β-strand	209	1	15
β-strand	214-219	6	17
β-strand	222-223	2	17
α-helix	225-227	3
β-strand	228-230	3	16
α-helix	231-233	3
β-strand	234-235	2	16
β-strand	241-250	10	16
α-helix	254-256	3
β-strand	257-262	6	17
β-strand	270-272	3	17

Chain F: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	18
β-strand	6-11	6	19
β-strand	21-22	2	20
β-strand	23-30	8	19
β-strand	31	1	18
β-strand	36-41	6	21
β-strand	44-45	2	21
β-strand	50-51	2	19
α-helix	52-54	3
β-strand	55-56	2	19
β-strand	62-67	6	19
β-strand	69-70	2	20
β-strand	78-83	6	21
β-strand	91-94	4	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, cw-4 CW*0401 alpha chain	A, E	protein	276	Homo sapiens	P10321 (AlphaFold model)
Beta-2 microglobulin	B, F	protein	100	Homo sapiens	P61769 (AlphaFold model)
HLA-Cw4-specific peptide	C, G	protein	9
Killer cell immunoglobulin-like receptor 2DL1	D	protein	225	Homo sapiens	P43626 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>1IM9_1 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, CW-4 CW*0401 ALPHA CHAIN (chains A, E)
MGSHSMRYFSTSVSWPGRGEPRFIAVGYVDDTQFVRFDSDAASPRGEPREPWVEQEGPEY
WDRETQKYKRQAQADRVNLRKLRGYYNQSEDGSHTLQRMFGCDLGPDGRLLRGYNQFAYD
GKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKETL
QRAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWK

Sequence of entity 2 (B, F), FASTA

>1IM9_2 Beta-2 microglobulin (chains B, F)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, G), FASTA

>1IM9_3 HLA-Cw4-specific peptide (chains C, G)
QYDDAVYKL

Sequence of entity 4 (D), FASTA

>1IM9_4 KILLER CELL IMMUNOGLOBULIN-LIKE RECEPTOR 2DL1 (chains D)
MHEGVHRKPSLLAHPGPLVKSEETVILQCWSDVMFEHFLLHREGMFNDTLRLIGEHHDGV
SKANFSISRMTQDLAGTYRCYGSVTHSPYQVSAPSDPLDIVIIGLYEKPSLSAQPGPTVL
AGENVTLSCSSRSSYDMYHLSREGEAHERRLPAGPKVNGTFQADFPLGPATHGGTYRCFG
SFHDSPYEWSKSSDPLLVSVTGNPSNSWPSPTEPSSKTGNPRHLH

Primary citation

Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1-HLA-Cw4 complex. Fan, Q.R., Long, E.O., Wiley, D.C. Nat Immunol (2001) 2:452-460. PubMed

Other PDB entries of the same protein (UniProt P10321 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6JTO 1.7 Å, Crystal structure of HLA-C05 in complex with a tumor mut10m peptide
5W6A 1.74 Å, HLA-C*06:02 presenting ARTELYRSL
4NT6 1.84 Å, HLA-C*0801 Crystal Structure
5W67 2.3 Å, HLA-C*06:02 presenting VRSRR(ABA)LRL
5VGD 2.32 Å, Crystal Structure of HLA-C*0501 in complex with SAE
3BZF 2.5 Å, The human non-classical major histocompatibility complex molecule HLA-E
6PAG 2.5 Å, Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA-C*07:02
5VGE 2.6 Å, Crystal structure of HLA-C*07:02 in complex with RYR peptide
1QQD 2.7 Å, Crystal structure of HLA-CW4, a ligand for the KIR2D natural killer cell inhibitory…
5W69 2.8 Å, HLA-C*06:02 presenting ARFNDLRFV
1EFX 3.0 Å, Structure of a complex between the human natural killer cell receptor KIR2DL2 and a…
6PA1 3.01 Å, Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*07:02

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