SAXSdb — 9p3m

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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 Homooligomer Protein × 16 其他Polymer 32 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 Chain I； UniProt 1–651 Chain J； UniProt 652–1138 Chain K； UniProt 1–651 Chain L； UniProt 652–1138 Chain M； UniProt 1–651 Chain N； UniProt 652–1138 Chain O； UniProt 1–651 Chain P； UniProt 652–1138	Not recorded	;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 ; × 8 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 8 ;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 ; × 8 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.43 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 9P3M	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 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 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 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
9P3X Structure of the ANDV dimer of tetramer at conformation I Deposited 2025-06-14	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 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	GP_ANDV
Isoform	—
PDB entities	1, 2
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 I； PDBConstruct 1–651； UniProt 1–651 Author chain K； PDBConstruct 1–651； UniProt 1–651 Author chain M； PDBConstruct 1–651； UniProt 1–651 Author chain O； 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 Author chain J； PDBConstruct 1–487； UniProt 652–1138 Author chain L； PDBConstruct 1–487； UniProt 652–1138 Author chain N； PDBConstruct 1–487； UniProt 652–1138 Author chain P； 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	9p3m
Deposition date deposition_date	2025-06-14
Structure title title	Structure of the ANDV dimer of tetramer at conformation II
Keywords keywords	viral glycoprotein, ANDV, hantavirus, dimer of tetramer, Gn and Gc, VIRAL PROTEIN; VIRAL PROTEIN
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	84.01 Å
Radius of gyration Rg (electron density) rg_electron	84.30 Å
Forward intensity I(0) i0	10860300000.00
Molecular weight molecular_weight	891260.0 kDa
Excluded volume excluded_volume	1116900 Å³
Envelope volume envelope_volume	1921400 Å³
Hydration-shell volume shell_volume	193680 Å³
Envelope diameter envelope_diameter	292.7 Å
Shell Rg shell_rg	78.76 Å
Envelope Rg envelope_rg	80.89 Å
Shape Rg shape_rg	84.30 Å
Total Rg total_rg	84.22 Å
Total atoms total_atoms	62312
Residues n_residues	7928
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	229.0 Å
Rg (real space) rg_real	80.82 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	1.0500e+10
I(0) uncertainty (real space) i0_real_error	2.0770e+08
Rg (reciprocal space) rg_reciprocal	82.06 Å
I(0) (reciprocal space) i0_reciprocal	10800000000.0000
Solution quality estimate total_estimate	0.9009
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	84.4 Å
Skewness Skewness skewness	0.396
Kurtosis Kurtosis kurtosis	-0.546
Angular range angular_range	— – 0.0950 Å⁻¹
Current regularization parameter α current_alpha	0.3405
Highest regularization parameter α highest_alpha	926300000.0000
Real-space data points n_real_points	20
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 0.981; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.025

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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	Glycoprotein N
Molecular weight formula_weight	72162.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	62312

MEGWYLVVLGVCYTLTLAMPKTIYELKMECPHTVGLGQGYIIGSTELGLISIEAASDIKLESSCNFDLHTTSMAQKSFTQVEWRKKSDTTDTTNAASTTFEAQTKTVNLRGTCILAPELYDTLKKVKKTVLCYDLTCNQTHCQPTVYLIAPVLTCMSIRSCMASVFTSRIQVIYEKTHCVTGQLIEGQCFNPAHTLTLSQPAHTYDTVTLPISCFFTPKKSEQLKVIKTFEGILTKTGCTENALQGYYVCFLGSHSEPLIVPSLEDIRSAEVVSRMLVHPRGEDHDAIQNSQSHLRIVGPITAKVPSTSSTDTLKGTAFAGVPMYSSLSTLVRNADPEFVFSPGIVPESNHSTCDKKTVPITWTGYLPISGEMEKVTGCTVFCTLAGPGASCEAYSENGIFNISSPTCLVNKVQRFRGSEQKINFICQRVDQDVVVYCNGQKKVILTKTLVIGQCIYTFTSLFSLMPDVAHSLAVELCVPGLHGWATVMLLSTFCFGWVLIPAVTLIILKCLRVLTFSCSHYTNESKFKFILEKVKIEYQKTMGSMVCDVCHHECETAKELESHRQSCINGQCPYCMTITEATESALQAHYSICKLTGRFQEALKKSLKKPEVKKGCYRTLGVFRYKSRCYVGLVWCLLLTCEIVIWAASA

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 2 Entity 2 polymer

Description description	Glycoprotein C
Molecular weight formula_weight	58843.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

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

ETPLMESGWSDTAHGVGEIPMKTDLELDFSLPSSSSYSYRRKLTNPANKEESIPFHFQMEKQVIHAEIQPLGHWMDATFNIKTAFHCYGACQKYSYPWQTSKCFFEKDYQYETGWGCNPGDCPGVGTGCTACGVYLDKLKSVGKAYKIISLKYTRKVCIQLGTEQTCKHIDANDCLVTPSVKVCIVGTVSKLQPSDTLLFLGPLEQGGIILKQWCTTSCAFGDPGDIMSTPSGMRCPEHTGSFRKICGFATTPVCEYQGNTISGYKRMMATKDSFQSFNLTEPHITTNKLEWIDPDGNTRDHVNLVLNRDVSFQDLSDNPCKVDLHTQAIEGAWGSGVGFTLTCTVGLTECPSFMTSIKACDLAMCYGSTVTNLARGSNTVKVVGKGGHSGSSFKCCHDTDCSSEGLLASAPHLERVTGFNQIDSDKVYDDGAPPCTFKCWFTKLGEWLLGILNGNWIVVVVLVVILILSIIMFSVLCPRRGHKKTVGSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK

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 3 Entity 3 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	8

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-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	748.7 kDa
Source method src_method	man
Copy count entity_count	8

Entity 5 Entity 5 branched

Description description	;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	748.7 kDa
Source method src_method	man
Copy count entity_count	8

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	8

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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	triclinic

Resolution resolution	3.43 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	72177

fit	/app/data/saxs_computation/p3/9p3m/9p3m.fit
pddf	/app/data/pr_computation/p3/9p3m/9p3m.pr.out
profile	/app/data/saxs_computation/p3/9p3m/9p3m.dat

Structure of the ANDV dimer of tetramer at conformation II

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 (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 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)