3d2u

Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

UL18 protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Beta-2-microglobulin × 1 （P61769） Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 （Q8NHL6） Actin × 1 （P60709） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 alpha-D-mannopyranose × 1 beta-D-mannopyranose × 1 alpha-L-fucopyranose × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Beta-2-microglobulin × 1 （P61769） Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 （Q8NHL6） Actin × 1 （P60709） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4A1U8_HCMV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–281； UniProt 21–301 Author chain E； PDBConstruct 1–281； UniProt 21–301

Beta-2-microglobulin

OrganismNot specified

UniProt P61769

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	UL18 protein × 1 （Q4A1U8） Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 （Q8NHL6） Actin × 1 （P60709） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 alpha-D-mannopyranose × 1 beta-D-mannopyranose × 1 alpha-L-fucopyranose × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	UL18 protein × 1 （Q4A1U8） Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 （Q8NHL6） Actin × 1 （P60709） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 21–119 Author chain F； PDBConstruct 1–99； UniProt 21–119

Leukocyte immunoglobulin-like receptor subfamily B member 1

OrganismNot specified

UniProt Q8NHL6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	UL18 protein × 1 （Q4A1U8） Beta-2-microglobulin × 1 （P61769） Actin × 1 （P60709） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 alpha-D-mannopyranose × 1 beta-D-mannopyranose × 1 alpha-L-fucopyranose × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	UL18 protein × 1 （Q4A1U8） Beta-2-microglobulin × 1 （P61769） Actin × 1 （P60709） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LIRB1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–198； UniProt 24–221 Author chain H； PDBConstruct 1–198； UniProt 24–221

Actin

OrganismNot specified

UniProt P60709

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	UL18 protein × 1 （Q4A1U8） Beta-2-microglobulin × 1 （P61769） Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 （Q8NHL6） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 alpha-D-mannopyranose × 1 beta-D-mannopyranose × 1 alpha-L-fucopyranose × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	UL18 protein × 1 （Q4A1U8） Beta-2-microglobulin × 1 （P61769） Leukocyte immunoglobulin-like receptor subfamily B member 1 × 1 （Q8NHL6） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACTB_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–9； UniProt 170–178 Author chain G； PDBConstruct 1–9； UniProt 170–178

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3d2u
Deposition date deposition_date	2008-05-08
Structure title title	Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor
Keywords keywords	;MHC class I homolog, Disease mutation, Glycation, Glycoprotein, Immune response, Immunoglobulin domain, MHC I, Pyrrolidone carboxylic acid, Secreted, Membrane, Phosphoprotein, Receptor, Transmembrane, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3d2u__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3d2u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d2u__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.40 Å
Rg (electron density)	27.54 Å
Total Rg	28.36 Å
Atom count	4681
Residues	571
Excluded volume	82616 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d2u__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d2u__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	UL18 protein
Molecular weight formula_weight	31665.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	9681

HVLRYGYTGIFDDTSHMTLTVVGIFDGQHFFTYHVQSSDKASSRANGTISWMANVSAAYPTYLDGERAKGDLIFNQTEQNLLELEIALGYRSQSVLTWTHECNTTENGSFVAGYEGFGWDGETLMELKDNLTLWTGPNYEISWLKQQKTYIDGKIKNISEGDTTIQRNYLKGNCTQWSVIYSGFQPPVTHPVVKGGVRNQNDNRAEAFCTSYGFFPGEIQITFIHYGDKVPEDSEPQCNPLLPTLDGTFHQGCYVAIFSNQNYTCRVTHGNWTVEIPISVT

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11748.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Entity 3 Entity 3 polymer

Description description	Leukocyte immunoglobulin-like receptor subfamily B member 1
Molecular weight formula_weight	22055.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTAPWITRIPQELVKKGQFPIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVTLQCDSQVAFDGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNSPYEWSLPSDLLELLVLG

Entity 4 Entity 4 polymer

Description description	Actin
Molecular weight formula_weight	1005.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,C

ALPHAILRL

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	13

Entity 6 Entity 6 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	beta-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	alpha-L-fucopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	362

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3d2ub_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d3d2ud1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d3d2ud2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d3d2uf_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d3d2uh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d3d2uh2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

CATH v4.4 (10 domains)

Domain ID domain_id	3d2uA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	3d2uA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3d2uB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3d2uD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3d2uD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3d2uE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	3d2uE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3d2uF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3d2uH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3d2uH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	52.366 Å
Unit-cell length b length_b	98.110 Å
Unit-cell length c length_c	172.147 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.210 Å
Low-resolution limit resolution_low	47.460 Å
R factor r_factor	—
R_work r_work	0.2410
R_free r_free	0.2590

Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor

1. Protein Identity and Related Structures Protein Identity & Related Structures

UL18 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Leukocyte immunoglobulin-like receptor subfamily B member 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3d2u__assembly_1__model_1

3d2u__assembly_1__model_1 | I(q)

3d2u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

CATH v4.4 (10 domains)

7. Citations (1)