5vod

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6

Method: X-RAY DIFFRACTION

▼

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 6	Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL130 × 1 （F5HCP3） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 9I6 heavy chain × 1 （S6B291） Fab 9I6 light chain × 1 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 14 其他Polymer 12	Envelope glycoprotein L × 2 （Q68674） Envelope glycoprotein UL128 × 2 （P16837） Envelope glycoprotein UL130 × 2 （F5HCP3） Envelope glycoprotein UL131A × 2 （F5HET4） Fab 9I6 heavy chain × 2 （S6B291） Fab 9I6 light chain × 2 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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 6	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL130 × 1 （F5HCP3） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 9I6 heavy chain × 1 （S6B291） Fab 9I6 light chain × 1 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 14 其他Polymer 12	Envelope glycoprotein H × 2 （Q6SW67） Envelope glycoprotein UL128 × 2 （P16837） Envelope glycoprotein UL130 × 2 （F5HCP3） Envelope glycoprotein UL131A × 2 （F5HET4） Fab 9I6 heavy chain × 2 （S6B291） Fab 9I6 light chain × 2 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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 6	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL130 × 1 （F5HCP3） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 9I6 heavy chain × 1 （S6B291） Fab 9I6 light chain × 1 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 14 其他Polymer 12	Envelope glycoprotein H × 2 （Q6SW67） Envelope glycoprotein L × 2 （Q68674） Envelope glycoprotein UL130 × 2 （F5HCP3） Envelope glycoprotein UL131A × 2 （F5HET4） Fab 9I6 heavy chain × 2 （S6B291） Fab 9I6 light chain × 2 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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 6	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL131A × 1 （F5HET4） Fab 9I6 heavy chain × 1 （S6B291） Fab 9I6 light chain × 1 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 14 其他Polymer 12	Envelope glycoprotein H × 2 （Q6SW67） Envelope glycoprotein L × 2 （Q68674） Envelope glycoprotein UL128 × 2 （P16837） Envelope glycoprotein UL131A × 2 （F5HET4） Fab 9I6 heavy chain × 2 （S6B291） Fab 9I6 light chain × 2 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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 6	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （Q68674） Envelope glycoprotein UL128 × 1 （P16837） Envelope glycoprotein UL130 × 1 （F5HCP3） Fab 9I6 heavy chain × 1 （S6B291） Fab 9I6 light chain × 1 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 14 其他Polymer 12	Envelope glycoprotein H × 2 （Q6SW67） Envelope glycoprotein L × 2 （Q68674） Envelope glycoprotein UL128 × 2 （P16837） Envelope glycoprotein UL130 × 2 （F5HCP3） Fab 9I6 heavy chain × 2 （S6B291） Fab 9I6 light chain × 2 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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 9I6 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 6	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 9I6 light chain × 1 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 14 其他Polymer 12	Envelope glycoprotein H × 2 （Q6SW67） Envelope glycoprotein L × 2 （Q68674） Envelope glycoprotein UL128 × 2 （P16837） Envelope glycoprotein UL130 × 2 （F5HCP3） Envelope glycoprotein UL131A × 2 （F5HET4） Fab 9I6 light chain × 2 （Q8TCD0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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 136–245； UniProt 132–241

Fab 9I6 light chain

Homo sapiens

UniProt Q8TCD0

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 6	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 9I6 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 × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 14 其他Polymer 12	Envelope glycoprotein H × 2 （Q6SW67） Envelope glycoprotein L × 2 （Q68674） Envelope glycoprotein UL128 × 2 （P16837） Envelope glycoprotein UL130 × 2 （F5HCP3） Envelope glycoprotein UL131A × 2 （F5HET4） Fab 9I6 heavy chain × 2 （S6B291） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8TCD0_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain L； PDBConstruct 125–241； UniProt 123–239

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	5vod
Deposition date deposition_date	2017-05-02
Structure title title	Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6
Keywords keywords	HCMV, neutralizing epitope, immunogen, viral entry, Pentamer, vaccine, IMMUNE SYSTEM, Viral Protein-Immune System complex; Viral Protein/Immune System
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5vod__assembly_1__model_1

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

Download this curve (.dat)

5vod__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vod__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	70.71 Å
Rg (electron density)	71.63 Å
Total Rg	71.51 Å
Atom count	14001
Residues	1727
Excluded volume	249000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vod__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vod__assembly_2__model_1`	tetradecameric （14）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

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	14001

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 9I6 heavy chain
Molecular weight formula_weight	30610.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MEFGLSWVFLVAILEGVHCEVQLVQSGAEVKKPGESLKISCRESGDTFPAYWIAWVRQMPGKGLEWMGIIYPIDSETTYSPSFQGQVTISADKSINTAYLQWSSLKASDSAIYYCARGTSTGLREAFHIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKSSGLEVLFQGPLGSAWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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 9I6 light chain
Molecular weight formula_weight	26621.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

METPAELLFLLLLWLPDTTGDVVMTQSPLSLAVTLGQPAYISCRSSQSLGYSDGNTYLNWFQQRPGQSPRRLIYEVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGTYYCMQGTHWPPMCSFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	3

Entity 9 Entity 9 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	910.8 kDa
Source method src_method	man
Copy count entity_count	2

Entity 10 Entity 10 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

▶

Unit-cell length a length_a	148.259 Å
Unit-cell length b length_b	208.820 Å
Unit-cell length c length_c	267.979 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	8

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	5.900 Å
Low-resolution limit resolution_low	45.710 Å
R factor r_factor	0.2600
R_work r_work	0.2580
R_free r_free	0.2990

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6

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 9I6 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 9I6 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

5vod__assembly_1__model_1

5vod__assembly_1__model_1 | I(q)

5vod__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 (10)

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