4zfz

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein

Method: X-RAY DIFFRACTION

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

Beta-2-microglobulin

Macaca mulatta

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Major histocompatibility complex class I × 1 5-mer lipopeptide from Protein Nef × 1 （P12482） ZINC ION × 6 1,2-ETHANEDIOL × 16 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CHLORIDE ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Major histocompatibility complex class I × 1 5-mer lipopeptide from Protein Nef × 1 （P12482） ZINC ION × 5 1,2-ETHANEDIOL × 15 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MYRISTIC ACID × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Major histocompatibility complex class I × 1 5-mer lipopeptide from Protein Nef × 1 （P12482） ZINC ION × 3 1,2-ETHANEDIOL × 16 CHLORIDE ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Major histocompatibility complex class I × 1 5-mer lipopeptide from Protein Nef × 1 （P12482） ZINC ION × 4 1,2-ETHANEDIOL × 18 CHLORIDE ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_MACMU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–100； UniProt 20–119 Author chain E； PDBConstruct 1–100； UniProt 20–119 Author chain H； PDBConstruct 1–100； UniProt 20–119 Author chain K； PDBConstruct 1–100； UniProt 20–119

5-mer lipopeptide from Protein Nef

OrganismNot specified

UniProt P12482

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Major histocompatibility complex class I × 1 Beta-2-microglobulin × 1 （Q6V7J5） ZINC ION × 6 1,2-ETHANEDIOL × 16 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CHLORIDE ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Major histocompatibility complex class I × 1 Beta-2-microglobulin × 1 （Q6V7J5） ZINC ION × 5 1,2-ETHANEDIOL × 15 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MYRISTIC ACID × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Major histocompatibility complex class I × 1 Beta-2-microglobulin × 1 （Q6V7J5） ZINC ION × 3 1,2-ETHANEDIOL × 16 CHLORIDE ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Major histocompatibility complex class I × 1 Beta-2-microglobulin × 1 （Q6V7J5） ZINC ION × 4 1,2-ETHANEDIOL × 18 CHLORIDE ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEF_SIVS4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–5； UniProt 2–6 Author chain F； PDBConstruct 1–5； UniProt 2–6 Author chain I； PDBConstruct 1–5； UniProt 2–6 Author chain L； PDBConstruct 1–5； UniProt 2–6

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	4zfz
Deposition date deposition_date	2015-04-22
Structure title title	Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein
Keywords keywords	MHC, lipopeptide, Antigen presentation, AIDS, 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.

4zfz__assembly_1__model_1

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

Download this curve (.dat)

4zfz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4zfz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.06 Å
Rg (electron density)	22.83 Å
Total Rg	23.66 Å
Atom count	3183
Residues	382
Excluded volume	55797 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4zfz__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4zfz__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4zfz__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4zfz__assembly_4__model_1`	trimeric （3）	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	Major histocompatibility complex class I
Molecular weight formula_weight	31687.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	13805

AGSHSMRYFSTTVSRPGRGEPRFIVVGYVDDTQFVRFDSDAASPKMEPRAPWMEQEGPEYWEEQTRRVKDAAQTFRVSLGNLRGYYNQSEAGSHTLQTMSGCDLGPDGRLLRGYYQQAYDGRDYIALNEDLRSWTAADEAAQNTQRKWEAAGVAEQWRAYLEGECLESLRRYLENGKETLQRAEPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPGGDGTFQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus macaque
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11731.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

AIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus macaque
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	5-mer lipopeptide from Protein Nef
Molecular weight formula_weight	403.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

GGAIS

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	65

Entity 6 Entity 6 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	810

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4zfzA01
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	4zfzA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfzB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfzD01
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	4zfzD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfzE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfzG01
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	4zfzG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfzH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfzJ01
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	4zfzJ02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4zfzK00
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	46.402 Å
Unit-cell length b length_b	85.179 Å
Unit-cell length c length_c	127.990 Å
Unit-cell angle α angle_alpha	89.20 °
Unit-cell angle β angle_beta	79.57 °
Unit-cell angle γ angle_gamma	90.02 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.763 Å
Low-resolution limit resolution_low	31.180 Å
R factor r_factor	0.1961
R_work r_work	0.1945
R_free r_free	0.2284

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein

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

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

5-mer lipopeptide from Protein Nef

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4zfz__assembly_1__model_1

4zfz__assembly_1__model_1 | I(q)

4zfz__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein

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

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

5-mer lipopeptide from Protein Nef

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

4zfz__assembly_1__model_1

4zfz__assembly_1__model_1 | I(q)

4zfz__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)