3D2U: UL18, a Peptide-Binding Viral MHC Mimic

Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor. Determined by X-ray diffraction at 2.21 Å resolution. Released 8 Jul 2008.

Method: X-ray diffraction
Resolution: 2.21 Å
Organisms: Human herpesvirus 5, Homo sapiens
Chains: 8
Atoms: 9,681
Mol. weight: 136.35 kDa
Ligands: FUC, BMA, MAN, NAG
Released: 8 Jul 2008

Explore 3D2U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D2U contains 33 α-helices and 108 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	1
β-strand	17-25	9	1
β-strand	28-36	9	1
β-strand	44-47	4	1
α-helix	51-58	8
α-helix	62-88	27
β-strand	95-104	10	1
β-strand	110-119	10	1
β-strand	122-127	6	1
β-strand	135	1	1
α-helix	143-147	5
α-helix	148-156	9
α-helix	161-171	11
α-helix	173-184	12
α-helix	186-188	3
β-strand	189	1	2
α-helix	190-191	2
β-strand	192-201	10	3
β-strand	204-214	11	3
β-strand	215	1	2
β-strand	220-226	7	4
β-strand	237-238	2	3
α-helix	239-241	3
β-strand	242-243	2	3
β-strand	249-258	10	3
β-strand	262-268	7	4
β-strand	273-279	7	4

Chain B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	87	1	9
β-strand	91-94	4	8

Chain D: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	10
β-strand	15-17	3	11
β-strand	22-27	6	10
β-strand	35-39	5	12
α-helix	45-49	5
α-helix	52-56	5
β-strand	59-62	4	10
α-helix	67-69	3
β-strand	71-77	7	12
β-strand	78	1	13
β-strand	84	1	13
α-helix	86-90	5
β-strand	91-93	3	12
β-strand	94-96	3	11
β-strand	99	1	9
β-strand	103-106	4	14
β-strand	111-112	2	15
β-strand	118-123	6	14
β-strand	126	1	5
β-strand	130-135	6	11
β-strand	144-146	3	11
β-strand	156-161	6	14
β-strand	171-178	8	11
β-strand	181-185	5	11
α-helix	188-191	4
β-strand	192-193	2	11
β-strand	195-196	2	15

Chain E: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-11	9	16
β-strand	17-25	9	16
β-strand	28-36	9	16
β-strand	44-47	4	16
α-helix	51-58	8
α-helix	62-87	26
β-strand	95-104	10	16
β-strand	110-119	10	16
β-strand	122-127	6	16
β-strand	135	1	16
α-helix	143-147	5
α-helix	148-155	8
α-helix	160-168	9
α-helix	169-173	5
α-helix	174-184	11
α-helix	186-188	3
β-strand	189	1	17
α-helix	190-191	2
β-strand	192-201	10	18
β-strand	204-214	11	18
β-strand	215	1	17
β-strand	220-226	7	4
β-strand	237-238	2	18
α-helix	239-241	3
β-strand	242-243	2	18
β-strand	249-258	10	18
β-strand	262-268	7	4
β-strand	273-279	7	4

Chain F: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	19
β-strand	3	1	20
α-helix	4-5	2
β-strand	6-11	6	21
β-strand	21-30	10	21
β-strand	31	1	20
β-strand	36-41	6	22
β-strand	44-45	2	22
α-helix	46	1
β-strand	50-51	2	21
β-strand	55-56	2	21
β-strand	62-70	9	21
β-strand	78-83	6	22
β-strand	87	1	23
β-strand	91-94	4	22

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	24
α-helix	4-6	3
β-strand	7-11	5	25
β-strand	15-17	3	26
β-strand	22-27	6	25
β-strand	35-39	5	27
α-helix	45-49	5
α-helix	52-55	4
β-strand	59-62	4	25
α-helix	67-69	3
β-strand	71-77	7	27
β-strand	78-79	2	28
β-strand	83-84	2	28
β-strand	85	1	24
α-helix	86-90	5
β-strand	91-93	3	27
β-strand	94-96	3	26
β-strand	99	1	23
β-strand	103-106	4	29
β-strand	111-113	3	30
β-strand	118-123	6	29
β-strand	126	1	19
β-strand	130-136	7	31
β-strand	144-146	3	31
β-strand	157-161	5	29
β-strand	171-177	7	31
β-strand	184-185	2	26
α-helix	187-191	5
β-strand	192-193	2	31
β-strand	195-197	3	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UL18 protein	A, E	protein	281	Human herpesvirus 5	P08560
Beta-2-microglobulin	B, F	protein	99	Homo sapiens	P61769 (AlphaFold model)
Leukocyte immunoglobulin-like receptor subfamily B member 1	D, H	protein	198	Homo sapiens	Q8NHL6 (AlphaFold model)
Actin	C, G	protein	9	Homo sapiens	P60709 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>3D2U_1 UL18 protein (chains A, E)
HVLRYGYTGIFDDTSHMTLTVVGIFDGQHFFTYHVQSSDKASSRANGTISWMANVSAAYP
TYLDGERAKGDLIFNQTEQNLLELEIALGYRSQSVLTWTHECNTTENGSFVAGYEGFGWD
GETLMELKDNLTLWTGPNYEISWLKQQKTYIDGKIKNISEGDTTIQRNYLKGNCTQWSVI
YSGFQPPVTHPVVKGGVRNQNDNRAEAFCTSYGFFPGEIQITFIHYGDKVPEDSEPQCNP
LLPTLDGTFHQGCYVAIFSNQNYTCRVTHGNWTVEIPISVT

Sequence of entity 2 (B, F), FASTA

>3D2U_2 Beta-2-microglobulin (chains B, F)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D, H), FASTA

>3D2U_3 Leukocyte immunoglobulin-like receptor subfamily B member 1 (chains D, H)
GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTAPWITRIPQELVKKGQF
PIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVTL
QCDSQVAFDGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSN
SPYEWSLPSDLLELLVLG

Sequence of entity 4 (C, G), FASTA

>3D2U_4 Actin (chains C, G)
ALPHAILRL

Ligands and cofactors

ID	Name	Formula	Copies
FUC	alpha-L-fucopyranose	C6 H12 O5	1
BMA	beta-D-mannopyranose	C6 H12 O6	1
MAN	alpha-D-mannopyranose	C6 H12 O6	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	13

Primary citation

Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor. Yang, Z., Bjorkman, P.J. Proc Natl Acad Sci U S A (2008) 105:10095-10100. DOI 10.1073/pnas.0804551105 · PubMed

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