SAXSdb — 6hpv

▼

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

Fetuin-B

Mus musculus

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 19–388	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；150 mM NaCl, 100 mM NaOAc, 20 mM Na-HEPES pH 7.8, 25% PEG 4000, 8% isopropanol	Resolution 2.30 Å R-free 0.253

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 6HPV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6HT9 Mouse fetuin-B in complex with crayfish astacin Deposited 2018-10-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 19–388（370 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6.	Resolution 3.10 Å R-free 0.270
6HT9 Mouse fetuin-B in complex with crayfish astacin Deposited 2018-10-03	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 19–388（370 aa）	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6.	Resolution 3.10 Å R-free 0.270
7AUW Inhibitory complex of human meprin beta with mouse fetuin-B. Deposited 2020-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–388（388 aa） Chain D 1–388（388 aa）	Not recorded	NA SODIUM ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；293 K；20.0% PEG smear medium, 0.1M ammonium sulfate, 0.05M magnesium sulfate heptahydrate, 0.1M bicine pH 9.3, 10% ethylene glycol.	Resolution 2.80 Å R-free 0.261

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FETUB_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–370； UniProt 19–388

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6hpv
Deposition date deposition_date	2018-09-22
Structure title title	Crystal structure of mouse fetuin-B
Keywords keywords	;Glycoprotein, cystatin domain, fertilization, egg coat, zona pellucida, hardening, metalloprotease inhibitor, ovastacin, ZP2, hydrolase inhibitor, liver-secreted protein ;; hydrolase inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.68 Å
Radius of gyration Rg (electron density) rg_electron	21.86 Å
Forward intensity I(0) i0	20456100.00
Molecular weight molecular_weight	33786.0 kDa
Excluded volume excluded_volume	42134 Å³
Envelope volume envelope_volume	51517 Å³
Hydration-shell volume shell_volume	20513 Å³
Envelope diameter envelope_diameter	76.9 Å
Shell Rg shell_rg	27.92 Å
Envelope Rg envelope_rg	22.09 Å
Shape Rg shape_rg	21.86 Å
Total Rg total_rg	22.67 Å
Total atoms total_atoms	4684
Residues n_residues	299
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

▼

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

Maximum dimension Dmax dmax	76.3 Å
Rg (real space) rg_real	22.73 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	2.0460e+07
I(0) uncertainty (real space) i0_real_error	3.0180e+05
Rg (reciprocal space) rg_reciprocal	22.72 Å
I(0) (reciprocal space) i0_reciprocal	20460000.0000
Solution quality estimate total_estimate	0.8749
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.417
Kurtosis Kurtosis kurtosis	-0.322
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3434000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.926

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Fetuin-B
Molecular weight formula_weight	41954.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4780

RSPPAPPLPQRPLSPLHPLGCNDSEVLAVAGFALQNINRDQKDGYMLSLNRVHDVREHYQEDMGSLFYLTLDVLETDCHVLSRKAQKDCKPRMFYESVYGQCKAMFHINKPRRVLYLPAYNCTLRPVSKRKTHTTCPDCPSPIDLSNPSALEAATESLAKFNSKSPSKKYELVKVTKAMNQWVSGPAYYVEYLIKEAPCTKSQASCSLQHSDSEPVGICQGSTVQSSLRHVPLIQPVEKSVTVTCEFFESQAQVPGDENPAVTQGPQKLPQKNTAPTSSPSVTAPRGSIQHLPELDDEKPEESKGGSPEEAFPVQLDLTTNPQGDTLDVSFLYLEPGDKKLVVLPFPGKEQRSAECPGPEKENNPLVLPPLEHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 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	2

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	85

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6hpvA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

▶

8. Citations (11)

Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition.

Iucrj (2019)

PMID: 30867929 · DOI: 10.1107/S2052252519001568 PRIMARY

Mammalian plasma fetuin-B is a selective inhibitor of ovastacin and meprin metalloproteinases.

Sci Rep (2019)

PMID: 30679641 · DOI: 10.1038/s41598-018-37024-5

Maternal malnourishment induced upregulation of fetuin-B blunts nephrogenesis in the low birth weight neonate.

Dev. Biol. (2018)

PMID: 30189195 · DOI: 10.1016/j.ydbio.2018.09.001

Recombinant fetuin-B protein maintains high fertilization rate in cumulus cell-free mouse oocytes.

Mol. Hum. Reprod. (2017)

PMID: 27733489 · DOI: 10.1093/molehr/gaw067

The novel adipokine/hepatokine fetuin B in severe human and murine diabetic kidney disease.

Diabetes Metab. (2017)

PMID: 28214129 · DOI: 10.1016/j.diabet.2017.01.005

Association of high fetuin-B concentrations in serum with fertilization rate in IVF: a cross-sectional pilot study.

Hum. Reprod. (2016)

PMID: 26759143 · DOI: 10.1093/humrep/dev340

Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism.

Cell Metab. (2015)

PMID: 26603189 · DOI: 10.1016/j.cmet.2015.09.023

Mammalian gamete fusion depends on the inhibition of ovastacin by fetuin-B.

Biol. Chem. (2014)

PMID: 25205729 · DOI: 10.1515/hsz-2014-0189

Fetuin-B, a liver-derived plasma protein is essential for fertilization.

Dev. Cell (2013)

PMID: 23562279 · DOI: 10.1016/j.devcel.2013.03.001

Tissue distribution and activity testing suggest a similar but not identical function of fetuin-B and fetuin-A.

Biochem. J. (2003)

PMID: 12943536 · DOI: 10.1042/BJ20030676

Fetuin-B, a second member of the fetuin family in mammals.

Biochem. J. (2000)

PMID: 10947975 · DOI: 10.1042/bj3500589

▶

Unit-cell length a length_a	67.710 Å
Unit-cell length b length_b	67.710 Å
Unit-cell length c length_c	197.810 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	47.878 Å
R factor r_factor	0.2255
R_work r_work	0.2241
R_free r_free	0.2529

fit	/app/data/saxs_computation/hp/6hpv/6hpv.fit
pddf	/app/data/pr_computation/hp/6hpv/6hpv.pr.out
profile	/app/data/saxs_computation/hp/6hpv/6hpv.dat

Crystal structure of mouse fetuin-B

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

Fetuin-B

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