SAXSdb — 7m22

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Envelope glycoprotein UL130 × 1 （A0A0G2TB82） UL131A × 1 （Q38M21） Neuropilin-2 × 1 （O60462） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C8BLJ3_HCMV
Isoform	—
PDB entities	1
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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Envelope protein UL128 × 1 （C8BLJ3） UL131A × 1 （Q38M21） Neuropilin-2 × 1 （O60462） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0G2TB82_HCMV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–189； UniProt 26–214

UL131A

Human cytomegalovirus

UniProt Q38M21

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Envelope protein UL128 × 1 （C8BLJ3） Envelope glycoprotein UL130 × 1 （A0A0G2TB82） Neuropilin-2 × 1 （O60462） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q38M21_HCMV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–111； UniProt 19–129

Neuropilin-2

Homo sapiens

UniProt O60462

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Envelope protein UL128 × 1 （C8BLJ3） Envelope glycoprotein UL130 × 1 （A0A0G2TB82） UL131A × 1 （Q38M21） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NRP2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain N； PDBConstruct 1–573； UniProt 23–595

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	7m22
Deposition date deposition_date	2021-03-15
Structure title title	Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2
Keywords keywords	HCMV pentamer, NRP2, cytomegalovirus, host receptor, VIRAL PROTEIN, VIRAL PROTEIN-HOST RECEPTOR complex; VIRAL PROTEIN/HOST RECEPTOR
Experimental Method method	ELECTRON MICROSCOPY

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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.

7m22__assembly_1__model_1

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

Download this curve (.dat)

7m22__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7m22__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.84 Å
Rg (electron density)	31.26 Å
Total Rg	31.81 Å
Atom count	6042
Residues	748
Excluded volume	106920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7m22__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 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
Atom count atom_count	6042

EECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADGRIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ

Source Source

Source organism organism	Human cytomegalovirus
Common name common_name	HHV-5
NCBI taxonomy ID ncbi_taxonomy_id	10359
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 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

Source Source

Source organism organism	Human cytomegalovirus
Common name common_name	HHV-5
NCBI taxonomy ID ncbi_taxonomy_id	10359
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 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

Source Source

Source organism organism	Human cytomegalovirus
Common name common_name	HHV-5
NCBI taxonomy ID ncbi_taxonomy_id	10359
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Neuropilin-2
Molecular weight formula_weight	65430.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

QPDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKHDCKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIKFTSDYARQGAGFSLRYEIFKTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDPLQVGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTDMAVAKDGFSARYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTGSLEVLFQ

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 5 Entity 5 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	2

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	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	3.65 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	203130

Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2

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

Neuropilin-2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7m22__assembly_1__model_1

7m22__assembly_1__model_1 | I(q)

7m22__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 (6)

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 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2

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

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

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

Neuropilin-2

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

7m22__assembly_1__model_1

7m22__assembly_1__model_1 | I(q)

7m22__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 (6)

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 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)