7t4r

CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11

Method: ELECTRON MICROSCOPY

▼

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

Thrombomodulin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	Envelope glycoprotein H × 2 （F5H9T3） Envelope glycoprotein L × 2 （Q71DN9） Envelope protein UL128 × 2 （Q38LY2） Envelope glycoprotein UL130 × 2 （Q38M07） Envelope protein UL131A × 2 （Q8AZ45） Fab 13H11 heavy chain × 2 Fab 13H11 light chain × 2 Fab MSL-109 light chain × 2 Fab MSL-109 heavy chain × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRBM_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–516； UniProt 1–516

Envelope glycoprotein H

Human betaherpesvirus 5

UniProt F5H9T3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	Thrombomodulin × 1 （P07204） Envelope glycoprotein L × 2 （Q71DN9） Envelope protein UL128 × 2 （Q38LY2） Envelope glycoprotein UL130 × 2 （Q38M07） Envelope protein UL131A × 2 （Q8AZ45） Fab 13H11 heavy chain × 2 Fab 13H11 light chain × 2 Fab MSL-109 light chain × 2 Fab MSL-109 heavy chain × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F5H9T3_HCMV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–715； UniProt 1–715 Author chain K； PDBConstruct 1–715； UniProt 1–715

Envelope glycoprotein L

Human betaherpesvirus 5

UniProt Q71DN9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	Thrombomodulin × 1 （P07204） Envelope glycoprotein H × 2 （F5H9T3） Envelope protein UL128 × 2 （Q38LY2） Envelope glycoprotein UL130 × 2 （Q38M07） Envelope protein UL131A × 2 （Q8AZ45） Fab 13H11 heavy chain × 2 Fab 13H11 light chain × 2 Fab MSL-109 light chain × 2 Fab MSL-109 heavy chain × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q71DN9_HCMV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–278； UniProt 1–278 Author chain L； PDBConstruct 1–278； UniProt 1–278

Envelope protein UL128

Human betaherpesvirus 5

UniProt Q38LY2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	Thrombomodulin × 1 （P07204） Envelope glycoprotein H × 2 （F5H9T3） Envelope glycoprotein L × 2 （Q71DN9） Envelope glycoprotein UL130 × 2 （Q38M07） Envelope protein UL131A × 2 （Q8AZ45） Fab 13H11 heavy chain × 2 Fab 13H11 light chain × 2 Fab MSL-109 light chain × 2 Fab MSL-109 heavy chain × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q38LY2_HCMV
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–171； UniProt 1–171 Author chain M； PDBConstruct 1–171； UniProt 1–171

Envelope glycoprotein UL130

Human betaherpesvirus 5

UniProt Q38M07

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	Thrombomodulin × 1 （P07204） Envelope glycoprotein H × 2 （F5H9T3） Envelope glycoprotein L × 2 （Q71DN9） Envelope protein UL128 × 2 （Q38LY2） Envelope protein UL131A × 2 （Q8AZ45） Fab 13H11 heavy chain × 2 Fab 13H11 light chain × 2 Fab MSL-109 light chain × 2 Fab MSL-109 heavy chain × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q38M07_HCMV
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–214； UniProt 1–214 Author chain N； PDBConstruct 1–214； UniProt 1–214

Envelope protein UL131A

Human betaherpesvirus 5

UniProt Q8AZ45

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 19	Thrombomodulin × 1 （P07204） Envelope glycoprotein H × 2 （F5H9T3） Envelope glycoprotein L × 2 （Q71DN9） Envelope protein UL128 × 2 （Q38LY2） Envelope glycoprotein UL130 × 2 （Q38M07） Fab 13H11 heavy chain × 2 Fab 13H11 light chain × 2 Fab MSL-109 light chain × 2 Fab MSL-109 heavy chain × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8AZ45_HCMV
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–129； UniProt 1–129 Author chain O； PDBConstruct 1–129； UniProt 1–129

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7t4r
Deposition date deposition_date	2021-12-10
Structure title title	CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11
Keywords keywords	Human Cytomegalovirus, glycoprotein complex, antibody complex, thrombomodulin, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex; VIRAL PROTEIN/Immune System
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7t4r__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7t4r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7t4r__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	75.15 Å
Rg (electron density)	75.01 Å
Total Rg	75.04 Å
Atom count	28717
Residues	3595
Excluded volume	510770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7t4r__assembly_1__model_1`	nonadecameric （19）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Thrombomodulin
Molecular weight formula_weight	55128.4 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	28717

MLGVLVLGALALAGLGFPAPAEPQPGGSQCVEHDCFALYPGPATFLNASQICDGLRGHLMTVRSSVAADVISLLLNGDGGVGRRRLWIGLQLPPGCGDPKRLGPLRGFQWVTGDNNTSYSRWARLDLNGAPLCGPLCVAVSAAEATVPSEPIWEEQQCEVKADGFLCEFHFPATCRPLAVEPGAAAAAVSITYGTPFAARGADFQALPVGSSAAVAPLGLQLMCTAPPGAVQGHWAREAPGAWDCSVENGGCEHACNAIPGAPRCQCPAGAALQADGRSCTASATQSCNDLCEHFCVPNPDQPGSYSCMCETGYRLAADQHRCEDVDDCILEPSPCPQRCVNTQGGFECHCYPNYDLVDGECVEPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQMFCNQTACPADCDPNTQASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALARHIGTDCDSGKVDGGDSGSGEPPPSPTPGSTLTPPAVGLVHSGGNSDYKDDDDK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	87311.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,K

MRPGLPSYLIILAVCLFSHLLSSRYGAEAVSEPLDKAFHLLLNTYGRPIRFLRENTTQCTYNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQRLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPIDLSIPHVWMPPQTTPHGWTESHTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSIDDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDAALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQVSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPNQITDITSLVRLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVHTTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFPDATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGISYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITVALNISLENCAFCQSALLEYDDTQGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDGTKLGPEQKLISEEDLNSAVDGSGLNDIFEAQKIEWHENLYFQGHHHHHHHH

Source Source

Source organism organism	Human betaherpesvirus 5
NCBI taxonomy ID ncbi_taxonomy_id	10359
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	30846.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVFEGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLRALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLGFELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDPPLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR

Source Source

Source organism organism	Human betaherpesvirus 5
NCBI taxonomy ID ncbi_taxonomy_id	10359
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Envelope protein UL128
Molecular weight formula_weight	19746.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,M

MSPKNLTPFLTALWLLLGHSRVPRVRAEECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ

Source Source

Source organism organism	Human betaherpesvirus 5
NCBI taxonomy ID ncbi_taxonomy_id	10359
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Envelope glycoprotein UL130
Molecular weight formula_weight	28866.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,N

MLRLLLRHHFHCLLLCAVWATPCLASPWFTLTANQNPSPPWSKLTYPKPHDAATFYCPFLYPSPPRSPSQFSGFQRVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPRTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIVGSENLYFQGSAWSHPQFEKGGGSGGGSGGGSAWSHPQFEK

Source Source

Source organism organism	Human betaherpesvirus 5
NCBI taxonomy ID ncbi_taxonomy_id	10359
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Envelope protein UL131A
Molecular weight formula_weight	15011.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,O

MRLCRVWLSVCLCAVVLGQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN

Source Source

Source organism organism	Human betaherpesvirus 5
NCBI taxonomy ID ncbi_taxonomy_id	10359
Host organism host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	Fab 13H11 heavy chain
Molecular weight formula_weight	26600.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,P

MKKNIAFLLASMFVFSIATNAYAQVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYIHWVRQAPGQGLEWMGIIHPSSGGTSYAQKFQGRVTMTRDTSTSTVSMDLSSLRSEDTAVYYCGRAFRILGLSDVFVNDWGQGTVVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Fab 13H11 light chain
Molecular weight formula_weight	25780.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,Q

MKKNIAFLLASMFVFSIATNAYADIQMTQSPSSLSASVGDRVTITCRASQGINNYLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTAFTLTILSLQPEDVATYYCQKYNSAPFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	Fab MSL-109 light chain
Molecular weight formula_weight	28355.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,R

MKKNIAFLLASMFVFSIATNAYADIVMTQSPLSLSVTPGEPASISCRSSQSLLHTNGYNYLDWYVQKPGQSPQLLIYLASNRASGVPDRFSGSGSGTDFTLKISRVETEDVGVYYCMQALQIPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECGLNDIFEAQKIEWHE

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 10 Entity 10 polymer

Description description	Fab MSL-109 heavy chain
Molecular weight formula_weight	27547.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,S

MKKNIAFLLASMFVFSIATNAYAEEQVLESGGGLVKPGGSLRLSCAASGFTFSPYSVFWVRQAPGKGLEWVSSINSDSTYKYYADSVKGRFTISRDNAENSIFLQMNSLRAEDTAVYYCARDRSYYAFSSGSLSDYYYGLDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 11 Entity 11 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	14

▶

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	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	504492

CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11

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

Thrombomodulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope glycoprotein L

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope protein UL128

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope glycoprotein UL130

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope protein UL131A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7t4r__assembly_1__model_1

7t4r__assembly_1__model_1 | I(q)

7t4r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer