SAXSdb — 9yq5

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

Hyaluronan synthase

Paramecium bursaria Chlorella virus CZ-2

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 A； UniProt 2–561	Not recorded	nanobody Nb872 × 1 nanobody Nb881 × 1 UGA URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.80 Å

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 9YQ5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SP6 Chlorella virus hyaluronan synthase Deposited 2021-11-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Mutation：D302N	Y01 CHOLESTEROL HEMISUCCINATE × 1 MN MANGANESE (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7SP7 Chlorella virus hyaluronan synthase inhibited by UDP Deposited 2021-11-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Not recorded	3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Sample incubated on grid 30s before blotting. Blot 4 seconds with force 4.	Resolution 3.10 Å
7SP8 Chlorella virus Hyaluronan Synthase bound to UDP-GlcNAc Deposited 2021-11-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Mutation：D302N	UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7SP9 Chlorella virus Hyaluronan Synthase in the GlcNAc-primed channel-closed state Deposited 2021-11-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Mutation：D302N	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7SPA Chlorella virus Hyaluronan Synthase in the GlcNAc-primed, channel-open state Deposited 2021-11-02	Different mutation/modification Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Mutation：D302N	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8SNC Chlorella virus Hyaluronan Synthase bound to GlcA extended GlcNAc primer Deposited 2023-04-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8SND Chlorella virus Hyaluronan Synthase bound to GlcNAc primer and UDP-GlcA Deposited 2023-04-27	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Mutation：D302N	3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 UGA URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8SNE Chlorella virus Hyaluronan Synthase bound to GlcA extended GlcNAc primer and UDP Deposited 2023-04-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Not recorded	UDP URIDINE-5'-DIPHOSPHATE × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9KQC Chlorella virus Hyaluronan Synthase bound to VNAR Deposited 2024-11-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–561（560 aa）	Not recorded	UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 MN MANGANESE (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
9YQ2 Chlorella virus hyaluronan synthase bound to DDM Deposited 2025-10-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 1 MN MANGANESE (II) ION × 2 LMT DODECYL-BETA-D-MALTOSIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9YQ4 Chlorella virus hyaluronan synthase bound to a proofreading UDP-GlcA Deposited 2025-10-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–561（560 aa）	Not recorded	UGA URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID × 1 MN MANGANESE (II) ION × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	M1H2Q1_9PHYC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–562； UniProt 2–561

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	9yq5
Deposition date deposition_date	2025-10-15
最后修订 last_revision	2025-12-10
Structure title title	Chlorella virus hyaluronan synthase bound to an inserted UDP-GlcA
Keywords keywords	Glycosyltransferase, Membrane Protein, Hyaluronan Synthase, Substrate, TRANSFERASE-IMMUNE SYSTEM complex; TRANSFERASE/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	36.64 Å
Radius of gyration Rg (electron density) rg_electron	36.76 Å
Forward intensity I(0) i0	107921000.00
Molecular weight molecular_weight	85524.0 kDa
Excluded volume excluded_volume	107860 Å³
Envelope volume envelope_volume	138060 Å³
Hydration-shell volume shell_volume	36045 Å³
Envelope diameter envelope_diameter	146.5 Å
Shell Rg shell_rg	36.89 Å
Envelope Rg envelope_rg	37.54 Å
Shape Rg shape_rg	36.77 Å
Total Rg total_rg	36.75 Å
Total atoms total_atoms	6023
Residues n_residues	742
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	136.4 Å
Rg (real space) rg_real	37.43 Å
Rg uncertainty (real space) rg_real_error	1.80 Å
I(0) (real space) i0_real	1.0790e+08
I(0) uncertainty (real space) i0_real_error	1.9350e+06
Rg (reciprocal space) rg_reciprocal	36.94 Å
I(0) (reciprocal space) i0_reciprocal	107900000.0000
Solution quality estimate total_estimate	0.7004
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.7 Å
Skewness Skewness skewness	0.774
Kurtosis Kurtosis kurtosis	0.036
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14320000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.391; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.206; Smooth: 0.721

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Hyaluronan synthase
Molecular weight formula_weight	65889.1 kDa
EC 编号 ec_number	2.4.1.212
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	6034

MGTSWRTIVSANLFAVGGALLMLAPAIVGYVFQWNIGVSAVWGISVYGVFVLGFYIAQIVFSEFNRMRLSDWISLRPDNWNATRVAVIIAGYREDPFMFKKCLESVRDSEYGNVARLICVIDGDEEEDLKMAEIYKQVYNDNVKKPGVVLCESENKNGSTIDSDVSKNICILQPHRGKRESLYTGFQLASMDPSVHAVVLIDSDTVLEKNAILEVVYPLSCDPNIKAVAGECKIWNTDTILSMLVSWRYFSAFNVERGAQSLWKTVQCVGGPLGAYTIDIINEIKDPWITQTFLGNKCTYGDNRRLTNEVLMRGKKIVYTPFAVGWSDSPTNVMRYIVQQTRWSKSWCREIWYTLGSAWKHGFSGIYLAFECMYQIMYFFLVMYLFSYIAIKADIRAQTATVLVSTLVTIIKSSYLALRAKNLKAFYFVLYTYVYFFCMIPARITAMFTMFDIAWGTRGGNAKMTIGARVWLWAKQFLITYMWWAGVLAAGVYSIVDNWYFDWADIQYRFALVGICSYLVFVSIVLVIYLIGKITTWNYTPLQKELIEERYLHNASENAPEVLEHHHHHHHHHH

来源 Source

来源生物 organism	Paramecium bursaria Chlorella virus CZ-2
NCBI Class编号 ncbi_taxonomy_id	1278251
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	nanobody Nb872
Molecular weight formula_weight	14783.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLVESGGGLVQAGGSLKVSCAASGRAFKTYRMAWFRQAPGKEREFVSGISALETTYYADSVKGRFTISRDNTKNTVSLQMDSLKPEDTAVYYCAARRYGGTDYTTTGSYDYWGQGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	Lama glama
通用名 common_name	llama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	nanobody Nb881
Molecular weight formula_weight	14956.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QVQLVESGGGLVQAGGSLRLACAASGRIFSSDTLAWFRRAPGKEREFVAASRWSGGGTDYADSVKGRFTFSRDNTFNTMCLEMNSLKPEDTAVYYCALRTARDSYYYTRNPTGYDYWGQGTQSSHHHHHHEPEA

来源 Source

来源生物 organism	Lama glama
通用名 common_name	llama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	;URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID ;
Molecular weight formula_weight	580.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHOLESTEROL HEMISUCCINATE
Molecular weight formula_weight	486.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	110407

fit	/app/data/saxs_computation/yq/9yq5/9yq5.fit
pddf	/app/data/pr_computation/yq/9yq5/9yq5.pr.out
profile	/app/data/saxs_computation/yq/9yq5/9yq5.dat

Chlorella virus hyaluronan synthase bound to an inserted UDP-GlcA

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

Hyaluronan synthase

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

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

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)