SAXSdb — 9x3k

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

Envelope glycoprotein

Dianlovirus menglaense

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 × 3 其他Polymer 6 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–662 Chain B； UniProt 1–662 Chain C； UniProt 1–662	Not recorded	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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 ; × 3 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 × 3	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.08 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 9X3K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X3J Glycoprotein of Mengla Virus with MR191 Fab bound Deposited 2025-10-09	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–662（662 aa） Chain B 1–662（662 aa） Chain E 1–662（662 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.47 Å

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

View Construct and Data Evidence

UniProt name	A0A3S8UVK3_9MONO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–662； UniProt 1–662 Author chain B； PDBConstruct 1–662； UniProt 1–662 Author chain C； PDBConstruct 1–662； UniProt 1–662

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	9x3k
Deposition date deposition_date	2025-10-09
Structure title title	apo state of Mengla Virus Glycoprotein
Keywords keywords	Mengla Virus Glycoprotein, 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	30.49 Å
Radius of gyration Rg (electron density) rg_electron	29.02 Å
Forward intensity I(0) i0	148688000.00
Molecular weight molecular_weight	97930.0 kDa
Excluded volume excluded_volume	123400 Å³
Envelope volume envelope_volume	159330 Å³
Hydration-shell volume shell_volume	43889 Å³
Envelope diameter envelope_diameter	89.4 Å
Shell Rg shell_rg	37.93 Å
Envelope Rg envelope_rg	28.93 Å
Shape Rg shape_rg	28.98 Å
Total Rg total_rg	30.04 Å
Total atoms total_atoms	6885
Residues n_residues	822
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	89.8 Å
Rg (real space) rg_real	30.26 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	1.4870e+08
I(0) uncertainty (real space) i0_real_error	2.0400e+06
Rg (reciprocal space) rg_reciprocal	30.36 Å
I(0) (reciprocal space) i0_reciprocal	148700000.0000
Solution quality estimate total_estimate	0.9100
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.5 Å
Skewness Skewness skewness	0.010
Kurtosis Kurtosis kurtosis	-0.677
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	83920000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.950

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein
Molecular weight formula_weight	73748.8 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	6885

MALAKKYLMRIFIISHYFLSYNYGFFLPIVKLDIQPENEIIKSPCNGVVKKTEDIHLMSLTLTGQKTASDPMAASKRWAFKEGVLPKTVAFTEGEEAKDCFNISIVDLQGRSLLLEAPSGIKDYPRCKSIHHIQGQNPHAKGNVLHLWGAFFLYDRIASTTMFKDKVFAEGNVAALVINKTVHHQIFKINKIPQNETIGSCNHTYWRSDAGDGFNTTLAVTNLAYVLSANESTKIFKQMQDDLRKRIENMTSSNLTTLSPEAISNSSDANSSATIAYGTSGASISATTRSATSTLTITTDGQMSPPPTPAPPSPSLKPSTDDIKTPTVLSTTSSSTRSKRSVTVAKQSSANPTGKQRGRGRKGPSTGTLTEEQIERVRMLIQKNVGRVNYNNLPLIAGLTALKKKRQVLETFSGEIELEELIGDEKLDSRFRENLKMILETLRNESYSHFELDIPKTAALKSPEETDPRIHMEYLGSGEEPIQSNGQTDTDCDPSLRIWTPNEEKLAAGVSWIPYFGPGAEGLYTMGLMQNQNDVVCRLRRLANQTAKSLDLLLRVTTEERTYSIINRHAIDFLLARWGGTCRVLGPECCIGVEDLTKNITDQIQQMRRDEQDEYEGWGKGGNWFNSQFGNWLNLGILIFLFLGIIIALSCVCRLFMNLTVY

来源 Source

来源生物 organism	Dianlovirus menglaense
NCBI Class编号 ncbi_taxonomy_id	3052181
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	1073.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 branched

Description description	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	586.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 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	3

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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	3.080 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.08 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	19463

fit	/app/data/saxs_computation/x3/9x3k/9x3k.fit
pddf	/app/data/pr_computation/x3/9x3k/9x3k.pr.out
profile	/app/data/saxs_computation/x3/9x3k/9x3k.dat

apo state of Mengla Virus Glycoprotein

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

Envelope 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

Refinement Refinement

冷冻电镜 EM 3D