SAXSdb — 9ucl

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

H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

Thermotoga maritima MSB8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	N4-nanobody-TAIL × 3 Nectin-4 × 3 （Q96NY8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXS1_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 118–321； UniProt 2–205 Author chain B； PDBConstruct 118–321； UniProt 2–205 Author chain C； PDBConstruct 118–321； UniProt 2–205

Nectin-4

Homo sapiens

UniProt Q96NY8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase × 3 （Q9WXS1） N4-nanobody-TAIL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NECT4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 2–116； UniProt 32–146 Author chain H； PDBConstruct 2–116； UniProt 32–146 Author chain I； PDBConstruct 2–116； UniProt 32–146

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	9ucl
Deposition date deposition_date	2025-04-04
Structure title title	CryoEM structure of IgV domain of human Nectin-4 with Trimbody
Keywords keywords	STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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.

9ucl__assembly_1__model_1

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

Download this curve (.dat)

9ucl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ucl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.19 Å
Rg (electron density)	44.62 Å
Total Rg	44.69 Å
Atom count	15549
Residues	2031
Excluded volume	278410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ucl__assembly_1__model_1`	nonameric （9）	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 (3)

Entity 1 Entity 1 polymer

Description description	H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Molecular weight formula_weight	36127.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	15549

MKEIAKIVAELLRGIARIIDDIKGRDREEEVEILAKAVEKTGKPEDVRLALEAAERGVTLDQAKAIAQILSMPNLTDEQKRGFVQSLLDDPSVSKEILAEAKKLNEHQAAKAEEAARKMEELFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTVIKALSVLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGCTEAAALEHHHHHH

Source Source

Source organism organism	Thermotoga maritima MSB8
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	N4-nanobody-TAIL
Molecular weight formula_weight	27671.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MAEVQLQASGGGFVQPGGSLRLSCAASGRFSAFYNMGWFRQAPGKEREFVSAISWSTNSAAYYADSVKGRFTISRDNSKNTVYLQMNSLRAEDTATYYCAASWHWNPPDHSWDAGYWGQGTLVAVVKTVEDAFLALLALEQHLGVQPADLAALAEKLNLSQLLELGELLKAAGHPLAPQVEALLKEKLKAASAAEAAGVIFQALVKDEELGKKILEWAKEFGTEEAKKAIEIAEKAYELYKKYLEHHHHHH

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nectin-4
Molecular weight formula_weight	13566.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

MGELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLEHHHHHH

Source Source

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

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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	2.430 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.43 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	567049

CryoEM structure of IgV domain of human Nectin-4 with Trimbody

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

H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

State in the Current Structure

Other States of the Same Protein in the Database

Nectin-4

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

9ucl__assembly_1__model_1

9ucl__assembly_1__model_1 | I(q)

9ucl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

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

7. Citations (1)

CryoEM structure of IgV domain of human Nectin-4 with Trimbody

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

H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nectin-4

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

9ucl__assembly_1__model_1

9ucl__assembly_1__model_1 | I(q)

9ucl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

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

7. Citations (1)