SAXSdb — 1s3a

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

NADH-ubiquinone oxidoreductase B8 subunit

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 0–98	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；300 K；Ionic strength (raw mmCIF value) 20mM phosphate, 50mM NaCl；Pressure ambient NMR sample composition：U-15N, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：U-15N, U-13C, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：U-15N, U-13C, 100% D2O \| 100% D2O	Resolution not provided

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 1S3A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5XTB Cryo-EM structure of human respiratory complex I matrix arm Deposited 2017-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain F 14–96（83 aa） Fragment：UNP RESIDUES 14-96	Not recorded	SF4 IRON/SULFUR CLUSTER × 6 FMN FLAVIN MONONUCLEOTIDE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5XTD Cryo-EM structure of human respiratory complex I Deposited 2017-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 45 PDB declaration: 45-meric	Chain F 14–96（83 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 6 FMN FLAVIN MONONUCLEOTIDE × 1 PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 9 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 CDL CARDIOLIPIN × 5 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
5XTH Cryo-EM structure of human respiratory supercomplex I1III2IV1 Deposited 2017-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 80 PDB declaration: 80-meric	Chain F 14–96（83 aa） Fragment：UNP RESIDUES 14-96	Not recorded	SF4 IRON/SULFUR CLUSTER × 6 FMN FLAVIN MONONUCLEOTIDE × 1 PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 12 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 4 CDL CARDIOLIPIN × 14 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 10 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 HEA HEME-A × 2 ZN ZINC ION × 1 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
5XTI Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2 Deposited 2017-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 138 PDB declaration: 138-meric	Chain BF 14–96（83 aa） Fragment：UNP RESIDUES 14-96 Chain F 14–96（83 aa） Fragment：UNP RESIDUES 14-96	Not recorded	SF4 IRON/SULFUR CLUSTER × 12 FMN FLAVIN MONONUCLEOTIDE × 2 PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 21 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 6 CDL CARDIOLIPIN × 19 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 14 CU COPPER (II) ION × 6 MG MAGNESIUM ION × 2 HEA HEME-A × 4 ZN ZINC ION × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 17.40 Å
9CWT Human kidney respiratory complex I Deposited 2024-07-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 45 PDB declaration: 45-meric	Chain F 1–99（99 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 6 FMN FLAVIN MONONUCLEOTIDE × 1 ZMP S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å
9I4I High resolution Cryo-EM structure of human complex I in mitochondria Deposited 2025-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 45 PDB declaration: 45-meric	Chain G 1–99（99 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 7 CDL CARDIOLIPIN × 6 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 7 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 6 FMN FLAVIN MONONUCLEOTIDE × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
9TI4 High resolution Cryo-EM structure of human complex I in mitochondria Deposited 2025-12-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 45 PDB declaration: 45-meric	Chain G 14–98（85 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 6 FMN FLAVIN MONONUCLEOTIDE × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 7 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 7 ZN ZINC ION × 1 CDL CARDIOLIPIN × 6 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25 mM HEPES-KOH pH=7.5, 50 mM KCl, 20 mM Mg(OAc)2, 0.01% (v/v) Lauryl Maltose Neopentyl Glycol (LMNG), 0.001 % cardiolipin, 0.001 % glycol-diosgenin (GDN, Sigma-Aldrich), 0.1mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.66 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NI8M_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–102； UniProt 0–98

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	1s3a
Deposition date deposition_date	2004-01-13
Structure title title	NMR Solution Structure of Subunit B8 from Human NADH-Ubiquinone Oxidoreductase Complex I (CI-B8)
Keywords keywords	CI-B8, NDUFA2, Complex I, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.45 Å
Radius of gyration Rg (electron density) rg_electron	11.89 Å
Forward intensity I(0) i0	481000000.00
Molecular weight molecular_weight	183710.0 kDa
Excluded volume excluded_volume	229630 Å³
Envelope volume envelope_volume	18225 Å³
Hydration-shell volume shell_volume	11666 Å³
Envelope diameter envelope_diameter	43.8 Å
Shell Rg shell_rg	19.11 Å
Envelope Rg envelope_rg	13.49 Å
Shape Rg shape_rg	11.85 Å
Total Rg total_rg	12.13 Å
Total atoms total_atoms	26030
Residues n_residues	1615
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	36.7 Å
Rg (real space) rg_real	12.35 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	4.8100e+08
I(0) uncertainty (real space) i0_real_error	4.2350e+06
Rg (reciprocal space) rg_reciprocal	12.35 Å
I(0) (reciprocal space) i0_reciprocal	481000000.0000
Solution quality estimate total_estimate	0.8353
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.3 Å
Skewness Skewness skewness	-0.009
Kurtosis Kurtosis kurtosis	-0.518
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	71970.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1s3aa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.22 — Mitochondrial ribosomal protein L51/S25/CI-B8 domain

CATH v4.4 (1 domains)

Domain ID domain_id	1s3aA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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8. Citations (1)

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Description description	NADH-ubiquinone oxidoreductase B8 subunit
Molecular weight formula_weight	11194.9 kDa
EC 编号 ec_number	1.6.5.3, 1.6.99.3
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	26030

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

fit	/app/data/saxs_computation/s3/1s3a/1s3a.fit
pddf	/app/data/pr_computation/s3/1s3a/1s3a.pr.out
profile	/app/data/saxs_computation/s3/1s3a/1s3a.dat

NMR Solution Structure of Subunit B8 from Human NADH-Ubiquinone Oxidoreductase Complex I (CI-B8)

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

NADH-ubiquinone oxidoreductase B8 subunit

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)