SAXSdb — 6yrb

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

Envelope polyprotein

Andes orthohantavirus

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–RNA Homooligomer Protein × 8 RNA 16 其他Polymer 4 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 375–484 Chain B； UniProt 375–484	Not recorded	;RNA (5'-D(())-R(PUPUPUP())-3') ; × 16 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 IOD* IODIDE ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.2M NaCl, 0.1M Hepes 7.5, 35% MPD	Resolution 2.35 Å R-free 0.266

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 6YRB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6Y6Q Structure of Andes virus envelope glycoprotein Gc in postfusion conformation Deposited 2020-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 652–1107（456 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；16% (w/v) PEG 4000, 10% (v/v) 2-propanol, 0.2M (NH4)2SO4, 0.1M Hepes pH 7.5	Resolution 2.70 Å R-free 0.287
6YRQ Crystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at pH 4.6 Deposited 2020-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 4 PDB declaration: octameric	Chain A 375–484（110 aa） Chain B 375–484（110 aa） Chain C 375–484（110 aa） Chain D 375–484（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2M CaCl2, 0.1M Na-acetate 4.6, 30% MPD	Resolution 1.90 Å R-free 0.230
8DBZ CryoEM structure of Hantavirus ANDV Gn(H) protein complex with 2Fabs ANDV-5 and ANDV-34 Deposited 2022-06-15	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 × 9 PDB declaration: nonameric	Chain A 22–374（353 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9P3I High-resolution in situ ANDV single tetramer structure Deposited 2025-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–651（651 aa） Chain B 652–1138（487 aa） Chain C 1–651（651 aa） Chain D 652–1138（487 aa） Chain E 1–651（651 aa） Chain F 652–1138（487 aa） Chain G 1–651（651 aa） Chain H 652–1138（487 aa）	Mutation：V535K Mutation：S1096L Mutation：V535K Mutation：S1096L Mutation：V535K Mutation：S1096L Mutation：V535K Mutation：S1096L	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.35 Å
9P3L Structure of ANDV dimer of tetramer at conformation III Deposited 2025-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–651（651 aa） Chain B 652–1138（487 aa） Chain C 1–651（651 aa） Chain D 652–1138（487 aa） Chain E 1–651（651 aa） Chain F 652–1138（487 aa） Chain G 1–651（651 aa） Chain H 652–1138（487 aa） Chain I 1–651（651 aa） Chain J 652–1138（487 aa） Chain K 1–651（651 aa） Chain L 652–1138（487 aa） Chain M 1–651（651 aa） Chain N 652–1138（487 aa） Chain O 1–651（651 aa） Chain P 652–1138（487 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9P3M Structure of the ANDV dimer of tetramer at conformation II Deposited 2025-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–651（651 aa） Chain B 652–1138（487 aa） Chain C 1–651（651 aa） Chain D 652–1138（487 aa） Chain E 1–651（651 aa） Chain F 652–1138（487 aa） Chain G 1–651（651 aa） Chain H 652–1138（487 aa） Chain I 1–651（651 aa） Chain J 652–1138（487 aa） Chain K 1–651（651 aa） Chain L 652–1138（487 aa） Chain M 1–651（651 aa） Chain N 652–1138（487 aa） Chain O 1–651（651 aa） Chain P 652–1138（487 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
9P3X Structure of the ANDV dimer of tetramer at conformation I Deposited 2025-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–651（651 aa） Chain B 652–1138（487 aa） Chain C 1–651（651 aa） Chain D 652–1138（487 aa） Chain E 1–651（651 aa） Chain F 652–1138（487 aa） Chain G 1–651（651 aa） Chain H 652–1138（487 aa） Chain I 1–651（651 aa） Chain J 652–1138（487 aa） Chain K 1–651（651 aa） Chain L 652–1138（487 aa） Chain M 1–651（651 aa） Chain N 652–1138（487 aa） Chain O 1–651（651 aa） Chain P 652–1138（487 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9P3Y Andes virus glycoprotein tetramer in complex with ADI-65534 Fab Deposited 2025-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–651（651 aa） Chain B 652–1138（487 aa） Chain C 1–651（651 aa） Chain D 652–1138（487 aa） Chain E 1–651（651 aa） Chain F 652–1138（487 aa） Chain G 1–651（651 aa） Chain H 652–1138（487 aa）	Mutation：V535K Mutation：S1096L Mutation：V535K Mutation：S1096L Mutation：V535K Mutation：S1096L Mutation：V535K Mutation：S1096L	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9E006_9VIRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–110； UniProt 375–484 Author chain B； PDBConstruct 1–110； UniProt 375–484

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	6yrb
Deposition date deposition_date	2020-04-20
Structure title title	Crystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at pH 7.5
Keywords keywords	class-II fusion protein hantavirus bunyavirus, VIRAL PROTEIN; VIRAL PROTEIN
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	23.21 Å
Radius of gyration Rg (electron density) rg_electron	22.91 Å
Forward intensity I(0) i0	13178400.00
Molecular weight molecular_weight	25013.0 kDa
Excluded volume excluded_volume	30078 Å³
Envelope volume envelope_volume	42268 Å³
Hydration-shell volume shell_volume	16403 Å³
Envelope diameter envelope_diameter	76.4 Å
Shell Rg shell_rg	28.30 Å
Envelope Rg envelope_rg	22.19 Å
Shape Rg shape_rg	22.82 Å
Total Rg total_rg	23.86 Å
Total atoms total_atoms	1683
Residues n_residues	209
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	71.3 Å
Rg (real space) rg_real	23.19 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.3180e+07
I(0) uncertainty (real space) i0_real_error	1.7180e+05
Rg (reciprocal space) rg_reciprocal	23.20 Å
I(0) (reciprocal space) i0_reciprocal	13180000.0000
Solution quality estimate total_estimate	0.9119
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	70.2 Å
Skewness Skewness skewness	0.163
Kurtosis Kurtosis kurtosis	-0.700
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1156000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Envelope polyprotein
Molecular weight formula_weight	15940.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1738

KVTGCTVFCTLAGPGASCEAYSENGIFNISSPTCLVNKVQRFRGSEQKINFICQRVDQDVVVYCNGQKKVILTKTLVIGQCIYTFTSLFSLMPDVAHSLAVELCVPGLHGGPFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

来源 Source

来源生物 organism	Andes orthohantavirus
NCBI Class编号 ncbi_taxonomy_id	1980456
宿主生物 host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	;RNA (5'-D(())-R(PUPUPUP*())-3') ;
Molecular weight formula_weight	1532.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D

AUUUA

Entity 3 Entity 3 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	55

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8. Citations (1)

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Unit-cell length a length_a	67.854 Å
Unit-cell length b length_b	67.854 Å
Unit-cell length c length_c	121.891 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	16

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.351 Å
Low-resolution limit resolution_low	37.699 Å
R factor r_factor	0.2280
R_work r_work	0.2260
R_free r_free	0.2655

fit	/app/data/saxs_computation/yr/6yrb/6yrb.fit
pddf	/app/data/pr_computation/yr/6yrb/6yrb.pr.out
profile	/app/data/saxs_computation/yr/6yrb/6yrb.dat

Crystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at pH 7.5

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

Envelope polyprotein

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)