SAXSdb — 9p3y

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

Glycoprotein N

Orthohantavirus andesense

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 16 其他Polymer 8 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 1–651 Chain B； UniProt 652–1138 Chain C； UniProt 1–651 Chain D； UniProt 652–1138 Chain E； UniProt 1–651 Chain F； UniProt 652–1138 Chain G； UniProt 1–651 Chain H； UniProt 652–1138	Mutation：V535K Mutation：S1096L	ADI-65534 variable heavy chain × 4 ADI-65534 variable light chain × 4 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 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

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 9P3Y	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 method 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
6YRB Crystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at pH 7.5 Deposited 2020-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 375–484（110 aa） Chain B 375–484（110 aa）	Not recorded	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
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 method 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 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 oligomeric state Different ligand/ion 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 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 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 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

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

View Construct and Data Evidence

UniProt name	GP_ANDV
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 1–651； UniProt 1–651 Author chain C； PDBConstruct 1–651； UniProt 1–651 Author chain E； PDBConstruct 1–651； UniProt 1–651 Author chain G； PDBConstruct 1–651； UniProt 1–651 Author chain B； PDBConstruct 1–487； UniProt 652–1138 Author chain D； PDBConstruct 1–487； UniProt 652–1138 Author chain F； PDBConstruct 1–487； UniProt 652–1138 Author chain H； PDBConstruct 1–487； UniProt 652–1138

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	9p3y
Deposition date deposition_date	2025-06-14
Structure title title	Andes virus glycoprotein tetramer in complex with ADI-65534 Fab
Keywords keywords	Gn/Gc, tetramer, hantavirus, prefusion, antibody, neutralizing, quaternary epitope, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/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	63.59 Å
Radius of gyration Rg (electron density) rg_electron	63.15 Å
Forward intensity I(0) i0	3506860000.00
Molecular weight molecular_weight	494700.0 kDa
Excluded volume excluded_volume	616750 Å³
Envelope volume envelope_volume	948220 Å³
Hydration-shell volume shell_volume	125190 Å³
Envelope diameter envelope_diameter	205.0 Å
Shell Rg shell_rg	65.69 Å
Envelope Rg envelope_rg	61.43 Å
Shape Rg shape_rg	63.20 Å
Total Rg total_rg	63.03 Å
Total atoms total_atoms	34636
Residues n_residues	4464
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	239.4 Å
Rg (real space) rg_real	66.32 Å
Rg uncertainty (real space) rg_real_error	1.71 Å
I(0) (real space) i0_real	3.5320e+09
I(0) uncertainty (real space) i0_real_error	6.7200e+07
Rg (reciprocal space) rg_reciprocal	63.74 Å
I(0) (reciprocal space) i0_reciprocal	3509000000.0000
Solution quality estimate total_estimate	0.8750
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	86.2 Å
Skewness Skewness skewness	0.507
Kurtosis Kurtosis kurtosis	0.302
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.5958
Highest regularization parameter α highest_alpha	217200000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.733; Stabil: 0.912; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.951

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	ADI-65534 variable heavy chain
Molecular weight formula_weight	14043.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K,M,O
Atom count atom_count	34636

QVQLVESGGGVVQPGRSLRLSCAASGFEFSSYAMHWVRQAPGKGLEWVAVTWFDVSKKDYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARNLIRYSVSYFPVHGMDVWGQGTTVTVSS

来源 Source

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	ADI-65534 variable light chain
Molecular weight formula_weight	12028.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,L,N,P

DIVMTQSPLSLPVTPGEPASISCRSSQSLLHTYGYNVLDWYLQRPGQSPQLLISLGSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQALHPFTFGGGTKVEIK

来源 Source

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	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Glycoprotein N
Molecular weight formula_weight	72192.6 kDa
Mutation mutation	V535K
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G

MEGWYLVVLGVCYTLTLAMPKTIYELKMECPHTVGLGQGYIIGSTELGLISIEAASDIKLESSCNFDLHTTSMAQKSFTQVEWRKKSDTTDTTNAASTTFEAQTKTVNLRGTCILAPELYDTLKKVKKTVLCYDLTCNQTHCQPTVYLIAPVLTCMSIRSCMASVFTSRIQVIYEKTHCVTGQLIEGQCFNPAHTLTLSQPAHTYDTVTLPISCFFTPKKSEQLKVIKTFEGILTKTGCTENALQGYYVCFLGSHSEPLIVPSLEDIRSAEVVSRMLVHPRGEDHDAIQNSQSHLRIVGPITAKVPSTSSTDTLKGTAFAGVPMYSSLSTLVRNADPEFVFSPGIVPESNHSTCDKKTVPITWTGYLPISGEMEKVTGCTVFCTLAGPGASCEAYSENGIFNISSPTCLVNKVQRFRGSEQKINFICQRVDQDVVVYCNGQKKVILTKTLVIGQCIYTFTSLFSLMPDVAHSLAVELCVPGLHGWATVMLLSTFCFGWVLIPAVTLIILKCLRVLTFSCSHYTNESKFKFILEKKKIEYQKTMGSMVCDVCHHECETAKELESHRQSCINGQCPYCMTITEATESALQAHYSICKLTGRFQEALKKSLKKPEVKKGCYRTLGVFRYKSRCYVGLVWCLLLTCEIVIWAASA

来源 Source

来源生物 organism	Orthohantavirus andesense
NCBI Class编号 ncbi_taxonomy_id	1980456
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Glycoprotein C
Molecular weight formula_weight	66793.6 kDa
Mutation mutation	S1096L
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

ETPLMESGWSDTAHGVGEIPMKTDLELDFSLPSSSSYSYRRKLTNPANKEESIPFHFQMEKQVIHAEIQPLGHWMDATFNIKTAFHCYGACQKYSYPWQTSKCFFEKDYQYETGWGCNPGDCPGVGTGCTACGVYLDKLKSVGKAYKIISLKYTRKVCIQLGTEQTCKHIDANDCLVTPSVKVCIVGTVSKLQPSDTLLFLGPLEQGGIILKQWCTTSCAFGDPGDIMSTPSGMRCPEHTGSFRKICGFATTPVCEYQGNTISGYKRMMATKDSFQSFNLTEPHITTNKLEWIDPDGNTRDHVNLVLNRDVSFQDLSDNPCKVDLHTQAIEGAWGSGVGFTLTCTVGLTECPSFMTSIKACDLAMCYGSTVTNLARGSNTVKVVGKGGHSGSSFKCCHDTDCSSEGLLASAPHLERVTGFNQIDSDKVYDDGAPPCTFKCWFTKLGEWLLGILNGNWIVVVVLVVILILSIIMFSVLCPRRGHKKTVGSGSALPGNPDHREMGETLPEEVGEYRQPSGGSVPVSPGPPSGLEPTSSSPYGGGSFNSSINNIHEMEIQLKDALEKNQQWLVYDQQREVYVKGLLAKIFELEKKTETAAGGGSHHHHHHHH

来源 Source

来源生物 organism	Orthohantavirus andesense
NCBI Class编号 ncbi_taxonomy_id	1980456
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	4

Entity 6 Entity 6 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (2)

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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	3.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	12483

fit	/app/data/saxs_computation/p3/9p3y/9p3y.fit
pddf	/app/data/pr_computation/p3/9p3y/9p3y.pr.out
profile	/app/data/saxs_computation/p3/9p3y/9p3y.dat

Andes virus glycoprotein tetramer in complex with ADI-65534 Fab

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

Glycoprotein N

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 (7)

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 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)