SAXSdb — 9z3q

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

Envelope glycoprotein H

Human gammaherpesvirus 8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 23–698	Not recorded	MLKH10 Light chain FV × 1 MLKH10 Heavy chain FV × 1 MLKH3 Light chain FV × 1 MLKH3 Heavy chain FV × 1 Envelope glycoprotein L × 1 （F5HDB7）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7；1x TBS cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.51 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	GH_HHV8P
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 27–702； UniProt 23–698

Envelope glycoprotein L

Human gammaherpesvirus 8

UniProt F5HDB7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain F； UniProt 21–167	Not recorded	MLKH10 Light chain FV × 1 MLKH10 Heavy chain FV × 1 MLKH3 Light chain FV × 1 MLKH3 Heavy chain FV × 1 Envelope glycoprotein H × 1 （F5HAK9）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7；1x TBS cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.51 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	GL_HHV8P
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 30–176； UniProt 21–167

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	9z3q
Deposition date deposition_date	2025-11-07
Structure title title	Cryo-EM structure of KSHV glycoprotein gHgL in complex with MLKH3 and MLKH10 FABs
Keywords keywords	KSHV, glycoprotein, Antibody, IMMUNE SYSTEM; 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	38.71 Å
Radius of gyration Rg (electron density) rg_electron	38.47 Å
Forward intensity I(0) i0	269249000.00
Molecular weight molecular_weight	133950.0 kDa
Excluded volume excluded_volume	167770 Å³
Envelope volume envelope_volume	218890 Å³
Hydration-shell volume shell_volume	48437 Å³
Envelope diameter envelope_diameter	144.2 Å
Shell Rg shell_rg	43.04 Å
Envelope Rg envelope_rg	38.61 Å
Shape Rg shape_rg	38.45 Å
Total Rg total_rg	38.80 Å
Total atoms total_atoms	9433
Residues n_residues	1192
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	129.7 Å
Rg (real space) rg_real	38.79 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	2.6920e+08
I(0) uncertainty (real space) i0_real_error	4.9430e+06
Rg (reciprocal space) rg_reciprocal	38.74 Å
I(0) (reciprocal space) i0_reciprocal	269200000.0000
Solution quality estimate total_estimate	0.8887
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.1 Å
Skewness Skewness skewness	0.334
Kurtosis Kurtosis kurtosis	-0.484
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51000000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.898

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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	MLKH10 Light chain FV
Molecular weight formula_weight	12427.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9433

DIVMTQSPDSLSVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRGSGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYNSPRFGGWTKVEIK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	MLKH10 Heavy chain FV
Molecular weight formula_weight	13144.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EVQLLESGGGVVRPGGSLRLSCAASGFTFDDYGMSWVRQSPGKGLEWVSGINWNGGSLSYADSIQGRFTISRDNAENSLYLQMHSLRAEDTALYYCARVQGSGSYNNFDYWGQGTLVTVSS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	MLKH3 Light chain FV
Molecular weight formula_weight	11538.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DIQLTQSPSSVSASVGDRVTISCRASQGISSWLVWYQQKPGKAPKPLIYAASSLQNGVPARFSGSGSGTDFTLTINSLQPEDFATYYCQQANSFPYTFGQGTKLEIK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	MLKH3 Heavy chain FV
Molecular weight formula_weight	13088.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

EVQLVQSGPEVKKPGSSVKVSCKASGDSFSSNTISWVRQAPGQGLEWMGRLITILGTANYAQKFQGRVTITADETATTAYMELSSLRSEDTAIYYCAISEGGYTYDSGSYIWGQGTLVTVSS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	80917.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDAMKRGLCCVLLLCGAVFVSPSASATGALPTTATTITRSATQLINGRTNLSIELEFNGTSFFLNWQNLLNVITEPALTELWTSAEVAEDLRVTLKKRQSLFFPNKTVVISGDGHRYTCEVPTSSQTYNITKGFNYSALPGHLGGFGINARLVLGDIFASKWSLFARDTPEYRVFYPMNVMAVKFSISIGNNESGVALYGVVSEDFVVVTLHNRSKEANETASHLLFGLPDSLPSLKGHATYDELTFARNAKYALVAILPKDSYQTLLTENYTRIFLNMTESTPLEFTRTIQTRIVSIEARRACAAQEAAPDIFLVLFQMLVAHFLVARGIAEHRFVEVDCVCRQYAELYFLRRISRLCMPTFTTVGYNHTTLGAVAATQIARVSATKLASLPRSSQETVLAMVQLGARDGAVPSSILEGIAMVVEHMYTAYTYVYTLGDTERKLMLDIHTVLTDSCPPKDSGVSEKLLRTYLMFTSMCTNIELGEMIARFSKPDSLNIYRAFSPCFLGLRYDLHPAKLRAEAPQSSALTRTAVARGTSGFAELLHALHLDSLNLIPAINCSKITADKIIATVPLPHVTYIISSEALSNAVVYEVSEIFLKSAMFISAIKPDCSGFNFSQIDRHIPIVYNISTPRRGCPLCDSVIMSYDESDGLQSLMYVTNERVQTNLFLDKSPFFDNNNLHIHYLWLRDNGTVVEIRGMYGSGSGHHHHHHGLNDIFEAQKIEWHE

来源 Source

来源生物 organism	Human gammaherpesvirus 8
NCBI Class编号 ncbi_taxonomy_id	37296
宿主生物 host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	18815.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MDAMKRGLCCVLLLCGAVFVSPSASDGIQYVALPCCAIQASAASTLPLFFAVHSIHFADPNHCNGVCIAKLRSKTGDITVETCVNGFNLRSFLVAVVRRLGSWASQENLRLLWYLQRSLTAYTVGFNATTADSSIHNVNIIIISVGKAMNRTGSVSGSQTRAKSSSRRAHAGQKGK

来源 Source

来源生物 organism	Human gammaherpesvirus 8
NCBI Class编号 ncbi_taxonomy_id	37296
宿主生物 host_organism	Homo sapiens

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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	3.51 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	75257

fit	/app/data/saxs_computation/z3/9z3q/9z3q.fit
pddf	/app/data/pr_computation/z3/9z3q/9z3q.pr.out
profile	/app/data/saxs_computation/z3/9z3q/9z3q.dat

Cryo-EM structure of KSHV glycoprotein gHgL in complex with MLKH3 and MLKH10 FABs

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

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein L

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

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Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)