4n90

Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody

Method: X-RAY DIFFRACTION

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

Tumor necrosis factor receptor superfamily member 10B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Tumor necrosis factor ligand superfamily member 10 × 1 （P50591） Fab light chain × 1 Fab heavy chain × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Tumor necrosis factor ligand superfamily member 10 × 1 （P50591） Fab light chain × 1 Fab heavy chain × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Tumor necrosis factor ligand superfamily member 10 × 1 （P50591） Fab light chain × 1 Fab heavy chain × 1 ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TR10B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain R； PDBConstruct 1–126； UniProt 57–182 Author chain S； PDBConstruct 1–126； UniProt 57–182 Author chain T； PDBConstruct 1–126； UniProt 57–182

Tumor necrosis factor ligand superfamily member 10

Homo sapiens

UniProt P50591

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Tumor necrosis factor receptor superfamily member 10B × 1 （O14763） Fab light chain × 1 Fab heavy chain × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Tumor necrosis factor receptor superfamily member 10B × 1 （O14763） Fab light chain × 1 Fab heavy chain × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Tumor necrosis factor receptor superfamily member 10B × 1 （O14763） Fab light chain × 1 Fab heavy chain × 1 ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TNF10_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 114–281 Author chain B； PDBConstruct 1–168； UniProt 114–281 Author chain C； PDBConstruct 1–168； UniProt 114–281

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	4n90
Deposition date deposition_date	2013-10-18
Structure title title	Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody
Keywords keywords	DR5, TRAIL, Agonist, antibody, cooperation, clustering, Apoptosis-Immune System complex; Apoptosis/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.

4n90__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4n90__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4n90__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	31.61 Å
Rg (electron density)	31.31 Å
Total Rg	31.90 Å
Atom count	5351
Residues	695
Excluded volume	94063 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4n90__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4n90__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4n90__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor receptor superfamily member 10B
Molecular weight formula_weight	14193.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S,T
Atom count atom_count	15934

TQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECVHKE

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

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor ligand superfamily member 10
Molecular weight formula_weight	19520.9 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

VRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

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

Entity 3 Entity 3 polymer

Description description	Fab light chain
Molecular weight formula_weight	23415.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 4 Entity 4 polymer

Description description	Fab heavy chain
Molecular weight formula_weight	23774.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

QVQLQESGPGLVKPSQTLSLTCTVSGGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYNPSLKSRVTISVDTSKKQFSLRLSSVTAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

Domain ID domain_id	4n90A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4n90B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4n90C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4n90D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90G02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90I02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90R01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	4n90R02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	4n90S01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	4n90S02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	4n90T01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	4n90T02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

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Unit-cell length a length_a	152.006 Å
Unit-cell length b length_b	152.006 Å
Unit-cell length c length_c	613.155 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2290
R_free r_free	0.2860

Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody

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

Tumor necrosis factor receptor superfamily member 10B

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor ligand superfamily member 10

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

4n90__assembly_3__model_1

4n90__assembly_3__model_1 | I(q)

4n90__assembly_3__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 (5)

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

6. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

7. Citations (1)

Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody

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

Tumor necrosis factor receptor superfamily member 10B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tumor necrosis factor ligand superfamily member 10

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

4n90__assembly_3__model_1

4n90__assembly_3__model_1 | I(q)

4n90__assembly_3__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 (5)

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

6. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

7. Citations (1)