SAXSdb — 7kbb

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

Envelope protein UL128

Human cytomegalovirus

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	2-18 Fab Heavy Chain × 1 2-18 Fab Light Chain × 1 Envelope glycoprotein UL130 × 1 （A0A0G2TB82） UL131A × 1 （Q38M21） 8I21 Fab Heavy Chain × 1 8I21 Fab Light Chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.02 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 7KBB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 C 28–171（144 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 C 28–171（144 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

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

View Construct and Data Evidence

UniProt name	C8BLJ3_HCMV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–144； UniProt 28–171

Envelope glycoprotein UL130

Human cytomegalovirus

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	2-18 Fab Heavy Chain × 1 2-18 Fab Light Chain × 1 Envelope protein UL128 × 1 （C8BLJ3） UL131A × 1 （Q38M21） 8I21 Fab Heavy Chain × 1 8I21 Fab Light Chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.02 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 7KBB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
8TEA HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab Deposited 2023-07-05	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 3.40 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	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–189； UniProt 26–214

UL131A

Human cytomegalovirus

UniProt Q38M21

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	2-18 Fab Heavy Chain × 1 2-18 Fab Light Chain × 1 Envelope protein UL128 × 1 （C8BLJ3） Envelope glycoprotein UL130 × 1 （A0A0G2TB82） 8I21 Fab Heavy Chain × 1 8I21 Fab Light Chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.02 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 7KBB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 E 19–129（111 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 E 19–129（111 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

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

View Construct and Data Evidence

UniProt name	Q38M21_HCMV
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–111； 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	7kbb
Deposition date deposition_date	2020-10-01
Structure title title	Cryo-EM structure of the HCMV pentamer bound by Fabs 2-18 and 8I21
Keywords keywords	HCMV pentamer, Fab, complex, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/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	36.25 Å
Radius of gyration Rg (electron density) rg_electron	36.08 Å
Forward intensity I(0) i0	133591000.00
Molecular weight molecular_weight	91081.0 kDa
Excluded volume excluded_volume	113090 Å³
Envelope volume envelope_volume	154180 Å³
Hydration-shell volume shell_volume	36477 Å³
Envelope diameter envelope_diameter	124.5 Å
Shell Rg shell_rg	41.53 Å
Envelope Rg envelope_rg	35.36 Å
Shape Rg shape_rg	36.03 Å
Total Rg total_rg	36.60 Å
Total atoms total_atoms	6422
Residues n_residues	797
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	119.8 Å
Rg (real space) rg_real	36.40 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	1.3360e+08
I(0) uncertainty (real space) i0_real_error	2.3140e+06
Rg (reciprocal space) rg_reciprocal	36.31 Å
I(0) (reciprocal space) i0_reciprocal	133600000.0000
Solution quality estimate total_estimate	0.8710
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.7 Å
Skewness Skewness skewness	0.327
Kurtosis Kurtosis kurtosis	-0.655
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17020000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.836; Smooth: 0.819

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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	2-18 Fab Heavy Chain
Molecular weight formula_weight	25640.5 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	6422

EVQLVQSGGGLVQPGGSLRVSCAASGFSFSDHDMDWVRQAPGKGFEWVGRSRNKDYSSTTEYAASVRGRFTISRHTSEDLLYLELNTVKTEDTAVYFCARGPHHSDRSGYYGGTFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	2-18 Fab Light Chain
Molecular weight formula_weight	23414.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIQMTQSPSSVSASVGDRVIITCRASQGISSWLAWYQQKPGRAPRLLIYDASTLESGVPSRFSGRGSGTEFTLTINSLQPEDFATYYCQQGNMFPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope protein UL128
Molecular weight formula_weight	16684.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ

来源 Source

来源生物 organism	Human cytomegalovirus
通用名 common_name	HHV-5
NCBI Class编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Envelope glycoprotein UL130
Molecular weight formula_weight	21761.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

SPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPRSPLQFSGFQQVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPQTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIV

来源 Source

来源生物 organism	Human cytomegalovirus
通用名 common_name	HHV-5
NCBI Class编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	UL131A
Molecular weight formula_weight	13005.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

QCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN

来源 Source

来源生物 organism	Human cytomegalovirus
通用名 common_name	HHV-5
NCBI Class编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	8I21 Fab Heavy Chain
Molecular weight formula_weight	25196.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

LVELVESGGGVVQPGRSLRLSCAASGFTFSSDGMHWVRQSPGRGLEWVAFISSDGSTPYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAMYFCAKDWALFRWLRTFDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	8I21 Fab Light Chain
Molecular weight formula_weight	23459.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ETVMTQSPATLSVSPGGRATLSCRASQSVGINLAWYQQKPGQAPRLLIYGASTRASGFPARFSGSGSGTEFTLTITSLQSEDFAVYYCQQYNDWPPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
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	—

Resolution resolution	4.02 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	249802

fit	/app/data/saxs_computation/kb/7kbb/7kbb.fit
pddf	/app/data/pr_computation/kb/7kbb/7kbb.pr.out
profile	/app/data/saxs_computation/kb/7kbb/7kbb.dat

Cryo-EM structure of the HCMV pentamer bound by Fabs 2-18 and 8I21

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

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

Entity 7 Entity 7 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)