SAXSdb — 8ze6

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

Spike glycoprotein

Pangolin coronavirus HKU4

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 × 4 其他Polymer 6 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 388–590 Chain C； UniProt 388–590	Not recorded	Dipeptidyl peptidase 4 × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Ammonium tartrate dibasic (pH 7.0) and 12% (wt/vol) PEG 3350.	Resolution 2.70 Å R-free 0.274

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 8ZE6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8ZDX Crystal structure of MjHKU4r-CoV-1 RBD bound to hDPP4 Deposited 2024-05-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 389–596（208 aa） Chain D 389–596（208 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES (pH 7.0) and 10% (wt/vol) PEG 6000	Resolution 2.60 Å R-free 0.252
9JMM Cryo-EM structure of the SE-PangolinCoV (MjHKU4r-CoV-1) RBD in complex with human DPP4 Deposited 2024-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 375–614（240 aa） Fragment：RBD	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9K9N Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain complexed with human CD26 Deposited 2024-10-27	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 Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 389–595（207 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0AAE8ZFM2_9BETC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 388–590 Author chain C； PDBConstruct 1–203； UniProt 388–590

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	8ze6
Deposition date deposition_date	2024-05-04
Structure title title	Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4
Keywords keywords	Virus protein and receptor complex, 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	52.00 Å
Radius of gyration Rg (electron density) rg_electron	52.59 Å
Forward intensity I(0) i0	669366000.00
Molecular weight molecular_weight	216260.0 kDa
Excluded volume excluded_volume	270700 Å³
Envelope volume envelope_volume	379690 Å³
Hydration-shell volume shell_volume	64729 Å³
Envelope diameter envelope_diameter	207.7 Å
Shell Rg shell_rg	49.89 Å
Envelope Rg envelope_rg	52.68 Å
Shape Rg shape_rg	52.53 Å
Total Rg total_rg	52.69 Å
Total atoms total_atoms	15274
Residues n_residues	1856
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	200.8 Å
Rg (real space) rg_real	52.55 Å
Rg uncertainty (real space) rg_real_error	3.38 Å
I(0) (real space) i0_real	6.6940e+08
I(0) uncertainty (real space) i0_real_error	1.4540e+07
Rg (reciprocal space) rg_reciprocal	51.56 Å
I(0) (reciprocal space) i0_reciprocal	668500000.0000
Solution quality estimate total_estimate	0.7644
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.2 Å
Skewness Skewness skewness	0.654
Kurtosis Kurtosis kurtosis	0.002
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	106500000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.423; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.739; Smooth: 0.924

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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	Dipeptidyl peptidase 4
Molecular weight formula_weight	84407.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	15431

RRTYTLTDYLKNTFRVKFYSLRWVSDHEYLYKQENNILLFNAEYGNSSIFLENSTFDEFGHSINDYSVSPDGQFILFEYNYVKKWRHSYTASYDIYDLHKRQLITEERIPNNTQWITWSPVGHKLAYVWHNDIYIKKEPNLQSQRITWTGKEDVIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTMQVPYPKAGAANPTVKLFVVNTDSLNSTANATSVQVVPPASVLIGDHYLCDVTWVNEERISLQWLRRIQNYSVLAICDYDKPTGRWASHVRQQHIESSTTGWVGRFKPSEPHFTSDGNSFYKIISNKEGYKHICHFQVDRENCTFITKGVWEVIGIEALTSDDLYYISNEYKGMPGGRNLYKIQLNDHTKVTCLSCELNTERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSSNDKELRVLEDNSALDKMLQDVQMPSKKLDFIIWNGIKLWYQMILPPHFDKLKKYPLLIDVYAGPCSQKADTVFRLNWATYLASTEKIIVASFDGRGSGYQGDKILHAINRRLGTLEVEDQIEAARQFTNMGFVDEKRIAIWGWSYGGYVTSMVLGAGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLEHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDAGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLPE

来源 Source

来源生物 organism	Manis javanica
NCBI Class编号 ncbi_taxonomy_id	9974
宿主生物 host_organism	Baculovirus expression vector pFastBac1-HM

Entity 2 Entity 2 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	22504.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DKECDFTPMLVGVPPQVYNFKRLVFTNCNYNLTKLLSLFMVNEFSCNGISPDAIARGCYSSLTVDYFAYPLSMRSYIQPGSAGDISLYNYKQSFANPTCRVLATAPANLTLTKPSAYGYFQKCSRVSGEHNSVETPLYINPGEYSICRSFSPYGFSEDGEVFRRQLTQYEGGGILVGVGAKLAMTDKLEMGFIISVQYGTDTN

来源 Source

来源生物 organism	Pangolin coronavirus HKU4
NCBI Class编号 ncbi_taxonomy_id	3027597
宿主生物 host_organism	Baculovirus expression vector pFastBac1-HM

Entity 3 Entity 3 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	6

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	man
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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8. Citations (1)

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Unit-cell length a length_a	96.532 Å
Unit-cell length b length_b	121.440 Å
Unit-cell length c length_c	110.624 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	47.490 Å
R factor r_factor	0.2440
R_work r_work	0.2424
R_free r_free	0.2736

fit	/app/data/saxs_computation/ze/8ze6/8ze6.fit
pddf	/app/data/pr_computation/ze/8ze6/8ze6.pr.out
profile	/app/data/saxs_computation/ze/8ze6/8ze6.dat

Crystal structure of MjHKU4r-CoV-1 RBD bound to MjDPP4

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

Spike 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

Diffraction experiment Diffraction

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)