2OZ4: Intercellular adhesion molecule 1

Structural Plasticity in IgSF Domain 4 of ICAM-1 Mediates Cell Surface Dimerization. Determined by X-ray diffraction at 2.7 Å resolution. Released 16 Oct 2007.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 5,601
Mol. weight: 76.43 kDa
Ligands: ZN, NAG
Released: 16 Oct 2007

Explore 2OZ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OZ4 contains 21 α-helices and 71 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 A: 8 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	191-192	2
β-strand	193-195	3	1
β-strand	199-201	3	2
β-strand	204-213	10	1
α-helix	218-220	3
β-strand	222-227	6	2
β-strand	230-231	2	2
β-strand	235-238	4	1
β-strand	242-251	10	1
α-helix	253-255	3
β-strand	257-267	11	2
β-strand	270-281	12	2
α-helix	284-286	3
β-strand	287-290	4	3
β-strand	294-296	3	4
β-strand	300-302	3	5
β-strand	303-306	4	3
β-strand	312-315	4	6
β-strand	326-327	2	3
β-strand	330-332	3	5
α-helix	335-337	3
β-strand	340-349	10	6
β-strand	354-363	10	6
β-strand	364-366	3	4
β-strand	367-370	4	7
α-helix	373-375	3
β-strand	379-383	5	8
β-strand	387-388	2	9
β-strand	395-397	3	7
α-helix	399-400	2
β-strand	401-406	6	8
β-strand	410-411	2	8
β-strand	418-419	2	9
α-helix	422-424	3
β-strand	426-434	9	8
β-strand	437-448	12	8

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
β-strand	10-12	3	16
β-strand	18-25	8	15
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	58-60	3	16
α-helix	62-64	3
β-strand	65	1	15
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-98	7	16
β-strand	103-104	2	16
β-strand	108-112	5	16
α-helix	116-117	2
β-strand	118	1	17
β-strand	121-125	5	18
β-strand	138-146	9	18
β-strand	147	1	17
β-strand	152-155	4	19
β-strand	164-166	3	18
α-helix	167-169	3
β-strand	170-171	2	18
β-strand	176-183	8	18
α-helix	186-188	3
β-strand	195-200	6	19
β-strand	205-210	6	19

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-25	7	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	84-90	7	11
α-helix	96	1
β-strand	97-98	2	11
β-strand	102-106	5	11
β-strand	111	1	12
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	145-150	6	14
β-strand	153-154	2	14
β-strand	159-163	5	13
α-helix	164-167	4
β-strand	173-182	10	13
α-helix	183-186	4
β-strand	191-197	7	14
α-helix	204	1
β-strand	205-210	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Intercellular adhesion molecule 1	A	protein	265	Homo sapiens	P05362 (AlphaFold model)
FAB fragment light chain	L	protein	214	Mus musculus	A0A0M4KEQ7 (AlphaFold model)
FAB fragment, heavy chain	H	protein	214	Mus musculus	P01868 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2OZ4_1 Intercellular adhesion molecule 1 (chains A)
VLPATPPQLVSPRVLEVDTQGTVVCSLDGLFPVSEAQVHLALGDQRLNPTVTYGNDSFSA
KASVSVTAEDEGTQRLTCAVILGNQSQETLQTVTIYSFPAPNVILTKPEVSEGTEVTVKC
EAHPRAKVTLNGVPAQPLGPRAQLLLKATPEDNGRSFSCSATLEVAGQLIHKNQTRELRV
LYGPRLDERDCPGNWTWPENSQQTPMCQAWGNPLPELKCLKDGTFPLPIGESVTVTRDLE
GTYLCRARSTQGEVTREVTVNVLSP

Sequence of entity 2 (L), FASTA

>2OZ4_2 FAB FRAGMENT LIGHT CHAIN (chains L)
DILLTQSPAILSVSPGERVSFSCRASQSIGTSIHWFQQRINGSPRLLIEYASESISGIPS
RFSGSGSGTDFTLTINSVESEDIADYYCQQSNVWPFTFGSGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H), FASTA

>2OZ4_3 FAB FRAGMENT, HEAVY CHAIN (chains H)
EVQLQQSGPELVQPGASVKISCKTSGYTFSEFTMHWVKQSHGKSLEWIGGINTINGGSSY
KQSFKDKATLTVDKSSSTAYMELNSLTSEDSAVYYCATKGFAYWGQGTLVTVSAAKTTPP
SVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSS
SVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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

Primary citation

Structural plasticity in Ig superfamily domain 4 of ICAM-1 mediates cell surface dimerization. Chen, X., Kim, T.D., Carman, C.V. et al. Proc Natl Acad Sci U S A (2007) 104:15358-15363. DOI 10.1073/pnas.0707406104 · PubMed

Other PDB entries of the same protein (UniProt P05362 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IAM 2.1 Å, Structure of the two amino-terminal domains of human intercellular adhesion molecule-1,…
7BG7 2.4 Å, HRV14 in complex with its receptor ICAM-1
5MZA 2.78 Å, The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1
1IC1 3.0 Å, The crystal structure for the N-terminal two domains of icam-1
1P53 3.06 Å, The Crystal Structure of ICAM-1 D3-D5 fragment
1D3L 3.25 Å, D1D2-icam-1 fully glycosylated, variation of D1-D2 interdomain angle in different…
1MQ8 3.3 Å, Crystal structure of alphaL I domain in complex with ICAM-1
3TCX 3.6 Å, Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain…
6S8U 3.67 Å, Structure of the PfEMP1 IT4var13 DBLbeta domain bound to ICAM-1
6EIT 3.9 Å, Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
1Z7Z 8.0 Å, Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi
1D3I 26.0 Å, cryo-EM structure of human rhinovirus 14 (HRV14) complexed with a two-domain fragment of…

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