SAXSdb — 8p4t

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

Glycoprotein

Mammarenavirus lujoense

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 × 9 其他Polymer 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 59–221 Chain B； UniProt 59–221 Chain C； UniProt 59–221 Chain SA； UniProt 1–58 Chain SB； UniProt 1–58 Chain SC； UniProt 1–58 Chain a； UniProt 222–454 Chain b； UniProt 222–454 Chain c； UniProt 222–454	Not recorded	;alpha-D-mannopyranose-(1-3)-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 ; × 3 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.96 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 8P4T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GH8 Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of neuropilin-2 Deposited 2018-05-06	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 × 2 PDB declaration: dimeric	Chain D 74–199（126 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.03M glycyl-glycyl-glycine, 25.9% PEG 6000, 0.09M Bis-Tris Propane pH 9.5	Resolution 2.44 Å R-free 0.311
6GH8 Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of neuropilin-2 Deposited 2018-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 74–199（126 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.03M glycyl-glycyl-glycine, 25.9% PEG 6000, 0.09M Bis-Tris Propane pH 9.5	Resolution 2.44 Å R-free 0.311

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

View Construct and Data Evidence

UniProt name	C5ILC1_9VIRU
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 59–221 Author chain B； PDBConstruct 1–163； UniProt 59–221 Author chain C； PDBConstruct 1–163； UniProt 59–221 Author chain a； PDBConstruct 1–233； UniProt 222–454 Author chain b； PDBConstruct 1–233； UniProt 222–454 Author chain c； PDBConstruct 1–233； UniProt 222–454 Author chain SA； PDBConstruct 1–58； UniProt 1–58 Author chain SB； PDBConstruct 1–58； UniProt 1–58 Author chain SC； PDBConstruct 1–58； UniProt 1–58

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	8p4t
Deposition date deposition_date	2023-05-23
Structure title title	The spike complex of the Lujo Virus
Keywords keywords	Spike complex, 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	34.50 Å
Radius of gyration Rg (electron density) rg_electron	34.38 Å
Forward intensity I(0) i0	301010000.00
Molecular weight molecular_weight	142350.0 kDa
Excluded volume excluded_volume	179320 Å³
Envelope volume envelope_volume	233770 Å³
Hydration-shell volume shell_volume	55788 Å³
Envelope diameter envelope_diameter	132.4 Å
Shell Rg shell_rg	41.45 Å
Envelope Rg envelope_rg	34.90 Å
Shape Rg shape_rg	34.34 Å
Total Rg total_rg	35.06 Å
Total atoms total_atoms	9976
Residues n_residues	1122
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	122.6 Å
Rg (real space) rg_real	34.49 Å
Rg uncertainty (real space) rg_real_error	1.28 Å
I(0) (real space) i0_real	3.0100e+08
I(0) uncertainty (real space) i0_real_error	4.9600e+06
Rg (reciprocal space) rg_reciprocal	34.50 Å
I(0) (reciprocal space) i0_reciprocal	301000000.0000
Solution quality estimate total_estimate	0.8402
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.6 Å
Skewness Skewness skewness	0.458
Kurtosis Kurtosis kurtosis	0.108
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	128600000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.645; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Glycoprotein
Molecular weight formula_weight	19017.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9976

SSLLSGFNLETVHFNMSLLSSIPMVSEQQHCIQHNHSSITFSLLTNKSDLEKCNFTRLQAVDRVIFDLFREFHHRVGDFPVTSDLKCSHNTSYRVIEYEVTKESLPRLQEAVSTLFPDLHLSEDRFLQIQAHDDKNCTGLHPLNYLRLLKENSETHYKVRKLM

来源 Source

来源生物 organism	Mammarenavirus lujoense
NCBI Class编号 ncbi_taxonomy_id	649188
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Glycoprotein
Molecular weight formula_weight	28267.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,b,c

KLFQWSLSDETGSPLPGGHCLERWLIFASDIKCFDNAAIAKCNKEHDEEFCDMLRLFDYNKASIAKLRGEASSSINLLSGRINAIISDTLLMRSSLKRLMGIPYCNYTKFWYLNHTKLGIHSLPRCWLVSNGSYLNETKFTHDMEDEADKLLTEMLKKEYVRRQEKTPITLMDILMFSVSFYMFSVTLCICNIPTHRHITGLPCPKPHRLRKNGTCACGFFKSINRSTGWAKHGGDYKDDDDKGSGT

来源 Source

来源生物 organism	Mammarenavirus lujoense
NCBI Class编号 ncbi_taxonomy_id	649188
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Glycoprotein
Molecular weight formula_weight	6502.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	SA,SB,SC

MGQIVAVFQAIPEILNEAINIVIIVIIMFTLIKGVFNLYKSGLFQLVIFLLLCGKRCD

来源 Source

来源生物 organism	Mammarenavirus lujoense
NCBI Class编号 ncbi_taxonomy_id	649188
宿主生物 host_organism	Homo sapiens

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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	894.8 kDa
Source method src_method	man
Copy count entity_count	3

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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	1235.1 kDa
Source method src_method	man
Copy count entity_count	3

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	3

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	21

Entity 8 Entity 8 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

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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	triclinic

Resolution resolution	2.96 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	87868

fit	/app/data/saxs_computation/p4/8p4t/8p4t.fit
pddf	/app/data/pr_computation/p4/8p4t/8p4t.pr.out
profile	/app/data/saxs_computation/p4/8p4t/8p4t.dat

The spike complex of the Lujo Virus

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

Glycoprotein

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 (8)

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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)