SAXSdb — 8tea

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

Envelope protein UL128

Human betaherpesvirus 5

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain C； UniProt 28–171	Not recorded	Envelope glycoprotein UL130 × 1 （A0A0G2TB82） UL131A × 1 （Q38M12） CS2pt1p2_A10L Fab light chain × 1 CS2pt1p2_A10L Fab heavy chain × 1 CS3pt1p4_C1L Fab heavy chain × 1 CS3pt1p4_C1L Fab light chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 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 8TEA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7T4Q CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 and 13H11 Deposited 2021-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain C 1–171（171 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5s before plunging	Resolution 2.90 Å
7T4R CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11 Deposited 2021-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain D 1–171（171 aa） Chain M 1–171（171 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5s before plunging	Resolution 3.30 Å
7T4S CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11 Deposited 2021-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain C 1–171（171 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5 seconds before plunging	Resolution 3.10 Å

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

View Construct and Data Evidence

UniProt name	Q38LY2_HCMV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 20–163； UniProt 28–171

Envelope glycoprotein UL130

Human betaherpesvirus 5

UniProt A0A0G2TB82

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain D； UniProt 26–214	Not recorded	Envelope protein UL128 × 1 （Q38LY2） UL131A × 1 （Q38M12） CS2pt1p2_A10L Fab light chain × 1 CS2pt1p2_A10L Fab heavy chain × 1 CS3pt1p4_C1L Fab heavy chain × 1 CS3pt1p4_C1L Fab light chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 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 8TEA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7KBB Cryo-EM structure of the HCMV pentamer bound by Fabs 2-18 and 8I21 Deposited 2020-10-01	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 26–214（189 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.02 Å
7M22 Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2 Deposited 2021-03-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 26–214（189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Grid was blotted with a force of -6 for 3 seconds	Resolution 3.65 Å
7M30 Cryo-EM structure of the HCMV pentamer bound by antibodies 1-103, 1-32 and 2-25 Deposited 2021-03-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 26–214（189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for six seconds with a force of "1" before plunging	Resolution 3.81 Å

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

View Construct and Data Evidence

UniProt name	A0A0G2TB82_HCMV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 20–208； UniProt 26–214

UL131A

Human betaherpesvirus 5

UniProt Q38M12

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain E； UniProt 19–129	Not recorded	Envelope protein UL128 × 1 （Q38LY2） Envelope glycoprotein UL130 × 1 （A0A0G2TB82） CS2pt1p2_A10L Fab light chain × 1 CS2pt1p2_A10L Fab heavy chain × 1 CS3pt1p4_C1L Fab heavy chain × 1 CS3pt1p4_C1L Fab light chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 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	Q38M12_HCMV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 20–130； UniProt 19–129

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	8tea
Deposition date deposition_date	2023-07-05
Structure title title	HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Keywords keywords	Virus, glycoprotein, antibody, 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	34.54 Å
Radius of gyration Rg (electron density) rg_electron	34.41 Å
Forward intensity I(0) i0	122233000.00
Molecular weight molecular_weight	86062.0 kDa
Excluded volume excluded_volume	106660 Å³
Envelope volume envelope_volume	138640 Å³
Hydration-shell volume shell_volume	35329 Å³
Envelope diameter envelope_diameter	120.3 Å
Shell Rg shell_rg	38.68 Å
Envelope Rg envelope_rg	34.40 Å
Shape Rg shape_rg	34.39 Å
Total Rg total_rg	34.77 Å
Total atoms total_atoms	6054
Residues n_residues	756
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	115.8 Å
Rg (real space) rg_real	34.59 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	1.2220e+08
I(0) uncertainty (real space) i0_real_error	2.1600e+06
Rg (reciprocal space) rg_reciprocal	34.56 Å
I(0) (reciprocal space) i0_reciprocal	122200000.0000
Solution quality estimate total_estimate	0.8778
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.2 Å
Skewness Skewness skewness	0.278
Kurtosis Kurtosis kurtosis	-0.571
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20940000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.857

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Envelope protein UL128
Molecular weight formula_weight	18940.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	6054

MEWSWVFLFFLSVTTGVHSEECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ

来源 Source

来源生物 organism	Human betaherpesvirus 5
NCBI Class编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein UL130
Molecular weight formula_weight	24018.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MEWSWVFLFFLSVTTGVHSSPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPRSPLQFSGFQQVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPQTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIV

来源 Source

来源生物 organism	Human betaherpesvirus 5
NCBI Class编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	UL131A
Molecular weight formula_weight	15262.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MEWSWVFLFFLSVTTGVHSQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN

来源 Source

来源生物 organism	Human betaherpesvirus 5
NCBI Class编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	CS2pt1p2_A10L Fab light chain
Molecular weight formula_weight	22850.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

QSALTQPPSASGTPGQRVTISCSGSSSNIGSNTVHWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSRSGTSASLAISGLRSEDEADYYCAAWDDSLNGRVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	CS2pt1p2_A10L Fab heavy chain
Molecular weight formula_weight	25916.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MEFGLSWVFLVALIKGVQCQVHLEESGGGLVKPGGSLRLSCVASGFSFSDYYMSWIRQAPGKGLEWLSYISPSGSPTSNADSMKGRFTISRDNARSSLYLQVHSLRVEDTAVYYCARDNTVFGVVTTPMDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	CS3pt1p4_C1L Fab heavy chain
Molecular weight formula_weight	23630.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

QVQLVQSGAEVKKPGSSVKVSCKASGGTFTDYALSWVRQAPGQGLEWMGGIIPVLGTPHYAQKFEDRVTIIADESTGTVFMALSSLRSDDTGMYYCARGVTHPYYYYAMDVWGQGTTITVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	CS3pt1p4_C1L Fab light chain
Molecular weight formula_weight	23239.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

QSALTQPASVSGSPGQSISISCTGTSSDVGAYDYVSWYQQHPGKAPRLIIYDVNKRPSGVPYRFSGSKSGTAASLTISGLQSEDEAVYYCGSYTSSSAFFYVFGTGTMVTVLRQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	8teaF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8teaG01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8teaI01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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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	3.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	71677

fit	/app/data/saxs_computation/te/8tea/8tea.fit
pddf	/app/data/pr_computation/te/8tea/8tea.pr.out
profile	/app/data/saxs_computation/te/8tea/8tea.dat

HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab

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

Envelope protein UL128

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein UL130

State in the Current Structure

Other States of the Same Protein in the Database

UL131A

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

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Entity 2 Entity 2 polymer

Polymer Polymer

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Entity 3 Entity 3 polymer

Polymer Polymer

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Entity 4 Entity 4 polymer

Polymer Polymer

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Entity 5 Entity 5 polymer

Polymer Polymer

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Entity 6 Entity 6 polymer

Polymer Polymer

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Entity 7 Entity 7 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)