5vob

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21

Method: X-RAY DIFFRACTION

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

Envelope glycoprotein H

Human cytomegalovirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 其他Polymer 1	Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL130 × 1 （F5HCP3） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 8I21 heavy chain × 1 （S6B291） Fab 8I21 light chain × 1 （Q6GMX0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GH_HCMVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–715； UniProt 1–715

Envelope glycoprotein L

Human cytomegalovirus (strain 5508)

UniProt Q68674

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 其他Polymer 1	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL130 × 1 （F5HCP3） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 8I21 heavy chain × 1 （S6B291） Fab 8I21 light chain × 1 （Q6GMX0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GL_HCMV8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–278； UniProt 1–278

Envelope glycoprotein UL128

Human cytomegalovirus (strain AD169)

UniProt P16837

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 其他Polymer 1	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL130 × 1 （F5HCP3） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 8I21 heavy chain × 1 （S6B291） Fab 8I21 light chain × 1 （Q6GMX0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UL128_HCMVA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–171； UniProt 1–171

Envelope glycoprotein UL130

Human cytomegalovirus (strain Merlin)

UniProt F5HCP3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 其他Polymer 1	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 8I21 heavy chain × 1 （S6B291） Fab 8I21 light chain × 1 （Q6GMX0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UL130_HCMVM
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–214； UniProt 1–214

Envelope glycoprotein UL131A

Human cytomegalovirus (strain Merlin)

UniProt F5HET4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 其他Polymer 1	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL130 × 1 （F5HCP3） Fab 8I21 heavy chain × 1 （S6B291） Fab 8I21 light chain × 1 （Q6GMX0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	U131A_HCMVM
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–129； UniProt 1–129

Fab 8I21 heavy chain

Homo sapiens

UniProt S6B291

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 其他Polymer 1	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL130 × 1 （F5HCP3） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 8I21 light chain × 1 （Q6GMX0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S6B291_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain H； PDBConstruct 131–246； UniProt 126–241

Fab 8I21 light chain

Homo sapiens

UniProt Q6GMX0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 其他Polymer 1	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL130 × 1 （F5HCP3） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 8I21 heavy chain × 1 （S6B291） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6GMX0_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain L； PDBConstruct 125–235； UniProt 126–236

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	5vob
Deposition date deposition_date	2017-05-02
Structure title title	Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21
Keywords keywords	HCMV, neutralizing epitope, immunogen, viral entry, Pentamer, vaccine, Viral Protein-Immune System complex; Viral Protein/Immune System
Experimental Method method	X-RAY DIFFRACTION

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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.

5vob__assembly_1__model_1

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

Download this curve (.dat)

5vob__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vob__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	59.51 Å
Rg (electron density)	59.77 Å
Total Rg	59.85 Å
Atom count	14099
Residues	1753
Excluded volume	250520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vob__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	82415.9 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	14099

MRPGLPSYLIILAVCLFSHLLSSRYGAEAVSEPLDKAFHLLLNTYGRPIRFLRENTTQCTYNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQRLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPIDLSIPHVWMPPQTTPHGWTESHTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSIDDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDAALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQVSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPNQITDITSLVRLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVHTTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFPDATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGISYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITVALNISLENCAFCQSALLEYDDTQGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDGSGSHHHHHH

Source Source

Source organism organism	Human cytomegalovirus
Common name common_name	HHV-5
NCBI taxonomy ID ncbi_taxonomy_id	295027
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	30846.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVFEGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLRALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLGFELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDPPLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR

Source Source

Source organism organism	Human cytomegalovirus (strain 5508)
Common name common_name	HHV-5
NCBI taxonomy ID ncbi_taxonomy_id	69168
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein UL128
Molecular weight formula_weight	19777.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSPKDLTPFLTTLWLLLGHSRVPRVRAEECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ

Source Source

Source organism organism	Human cytomegalovirus (strain AD169)
Common name common_name	HHV-5
NCBI taxonomy ID ncbi_taxonomy_id	10360
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Envelope glycoprotein UL130
Molecular weight formula_weight	28664.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MLRLLLRHHFHCLLLCAVWATPCLASPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPRSPLQFSGFQRVSTGPECRNETLYLLYNREGQTLVERSSTWVKKVIWYLSGRNQTILQRMPRTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRDYSVSFQVRLTFTEANNQTYTFCTHPNLIVGSENLYFQAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source Source

Source organism organism	Human cytomegalovirus (strain Merlin)
Common name common_name	HHV-5
NCBI taxonomy ID ncbi_taxonomy_id	295027
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Envelope glycoprotein UL131A
Molecular weight formula_weight	15011.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MRLCRVWLSVCLCAVVLGQCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRRGGTNKRTTFNAAGSLAPHARSLEFSVRLFAN

Source Source

Source organism organism	Human cytomegalovirus (strain Merlin)
Common name common_name	HHV-5
NCBI taxonomy ID ncbi_taxonomy_id	295027
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Fab 8I21 heavy chain
Molecular weight formula_weight	30873.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MEFGLSWVFLVAILEGVHCLVELVESGGGVVQPGRSLRLSCAASGFTFSSDGMHWVRQSPGRGLEWVAFISSDGSTPYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAMYFCAKDWALFRWLRTFDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKSSGLEVLFQGPLGSAWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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 7 Entity 7 polymer

Description description	Fab 8I21 light chain
Molecular weight formula_weight	25714.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

METPAELLFLLLLWLPDTTGETVMTQSPATLSVSPGGRATLSCRASQSVGINLAWYQQKPGQAPRLLIYGASTRASGFPARFSGSGSGTEFTLTITSLQSEDFAVYYCQQYNDWPPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 8 Entity 8 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 9 Entity 9 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	10

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5vobl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5vobl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id	5vobH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vobL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vobL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	124.163 Å
Unit-cell length b length_b	145.422 Å
Unit-cell length c length_c	173.658 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.020 Å
Low-resolution limit resolution_low	49.350 Å
R factor r_factor	0.1920
R_work r_work	0.1900
R_free r_free	0.2370

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21

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

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 glycoprotein 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 glycoprotein 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

Fab 8I21 heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fab 8I21 light chain

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

5vob__assembly_1__model_1

5vob__assembly_1__model_1 | I(q)

5vob__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

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