SAXSdb — 4zfz

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 20–119	Not recorded	Major histocompatibility complex class I × 1 5-mer lipopeptide from Protein Nef × 1 （P12482） ZN ZINC ION × 6 EDO 1,2-ETHANEDIOL × 16 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 20–119	Not recorded	Major histocompatibility complex class I × 1 5-mer lipopeptide from Protein Nef × 1 （P12482） ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 15 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain H； UniProt 20–119	Not recorded	Major histocompatibility complex class I × 1 5-mer lipopeptide from Protein Nef × 1 （P12482） ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 16 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
4	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain K； UniProt 20–119	Not recorded	Major histocompatibility complex class I × 1 5-mer lipopeptide from Protein Nef × 1 （P12482） ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 18 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4ZFZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JTT Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 Deposited 2009-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Bis-Tris pH 5.5, 2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.255
3JTT Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 Deposited 2009-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Bis-Tris pH 5.5, 2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.255
3JTT Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 Deposited 2009-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Bis-Tris pH 5.5, 2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.255
3RWC Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.249
3RWC Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.249
3RWD rhesus macaque MHC class I molecule Mamu-B*17-IW11 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.277
3RWD rhesus macaque MHC class I molecule Mamu-B*17-IW11 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.277
3RWE rhesus macaque MHC class I molecule Mamu-B*17-FW9 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.251
3RWF Rhesus macaque MHC class I molecule Mamu-B*17-QW9 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.246
3RWG Rhesus macaque MHC class I molecule Mamu-B*17-MW9 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	XPE 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.237
3RWH Rhesus macaque MHC class I molecule Mamu-B*17-MF8 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.272
3RWH Rhesus macaque MHC class I molecule Mamu-B*17-MF8 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.272
3RWI Rhesus macaque MHC class I molecule Mamu-B*17-GW10 Deposited 2011-05-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.01 Å R-free 0.210
6IWG Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein Deposited 2018-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–119（100 aa）	Not recorded	NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 18 BO3 BORIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；100mM MIB, 25% PEG 1500	Resolution 1.80 Å R-free 0.215
6IWH Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with C14-GGGI lipopeptide Deposited 2018-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–119（100 aa）	Not recorded	NA SODIUM ION × 5 EDO 1,2-ETHANEDIOL × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；200mM Sodium fluoride, 100mM Bis-Tris propane, 20% PEG 3350	Resolution 1.95 Å R-free 0.217
6LAH Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylcholine Deposited 2019-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–119（100 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.87 Å R-free 0.230
6LAH Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylcholine Deposited 2019-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–119（100 aa）	Not recorded	ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 19 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.87 Å R-free 0.230
6LAM Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylethanolamine Deposited 2019-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–119（100 aa）	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 10 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.15；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.80 Å R-free 0.229
6LAM Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylethanolamine Deposited 2019-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–119（100 aa）	Not recorded	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 16 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.15；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.80 Å R-free 0.229
6LB2 Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with mono-acyl glycerol Deposited 2019-11-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–119（100 aa）	Not recorded	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 22 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.69 Å R-free 0.227
6LB2 Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with mono-acyl glycerol Deposited 2019-11-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–119（100 aa）	Not recorded	ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 19 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.69 Å R-free 0.227
6LT6 Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with lysophosphatidylcholine Deposited 2020-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–119（100 aa）	Not recorded	EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1 EDO 1,2-ETHANEDIOL × 8 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1M Bis-Tris propane, 0.2M Sodium malonate dibasic monohydrate, 20% PEG3350	Resolution 2.15 Å R-free 0.232
7BYD Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104 Deposited 2020-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 20–119（100 aa）	Not recorded	IOD IODIDE ION × 9 EDO 1,2-ETHANEDIOL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CA CALCIUM ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5 and 20% PEG3350	Resolution 2.80 Å R-free 0.250
7BYD Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104 Deposited 2020-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 20–119（100 aa）	Not recorded	IOD IODIDE ION × 10 EDO 1,2-ETHANEDIOL × 3 MYR MYRISTIC ACID × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5 and 20% PEG3350	Resolution 2.80 Å R-free 0.250

15 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 2–6	Not recorded	Major histocompatibility complex class I × 1 Beta-2-microglobulin × 1 （Q6V7J5） ZN ZINC ION × 6 EDO 1,2-ETHANEDIOL × 16 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 2–6	Not recorded	Major histocompatibility complex class I × 1 Beta-2-microglobulin × 1 （Q6V7J5） ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 15 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain I； UniProt 2–6	Not recorded	Major histocompatibility complex class I × 1 Beta-2-microglobulin × 1 （Q6V7J5） ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 16 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
4	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain L； UniProt 2–6	Not recorded	Major histocompatibility complex class I × 1 Beta-2-microglobulin × 1 （Q6V7J5） ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 18 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	53.72 Å
Radius of gyration Rg (electron density) rg_electron	54.18 Å
Forward intensity I(0) i0	530623000.00
Molecular weight molecular_weight	181420.0 kDa
Excluded volume excluded_volume	222730 Å³
Envelope volume envelope_volume	339420 Å³
Hydration-shell volume shell_volume	57125 Å³
Envelope diameter envelope_diameter	190.3 Å
Shell Rg shell_rg	50.62 Å
Envelope Rg envelope_rg	52.50 Å
Shape Rg shape_rg	54.19 Å
Total Rg total_rg	54.05 Å
Total atoms total_atoms	12713
Residues n_residues	1528
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	178.4 Å
Rg (real space) rg_real	54.18 Å
Rg uncertainty (real space) rg_real_error	2.54 Å
I(0) (real space) i0_real	5.3060e+08
I(0) uncertainty (real space) i0_real_error	1.2010e+07
Rg (reciprocal space) rg_reciprocal	53.33 Å
I(0) (reciprocal space) i0_reciprocal	530000000.0000
Solution quality estimate total_estimate	0.8159
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.2 Å
Skewness Skewness skewness	0.503
Kurtosis Kurtosis kurtosis	-0.353
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24020000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.144

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Macaca mulatta
通用名 common_name	Rhesus macaque
NCBI Class编号 ncbi_taxonomy_id	9544
宿主生物 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

来源 Source

来源生物 organism	Macaca mulatta
通用名 common_name	Rhesus macaque
NCBI Class编号 ncbi_taxonomy_id	9544
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/zf/4zfz/4zfz.fit
pddf	/app/data/pr_computation/zf/4zfz/4zfz.pr.out
profile	/app/data/saxs_computation/zf/4zfz/4zfz.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 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

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)