6a3v

Complex structure of human 4-1BB and 4-1BBL

Method: X-RAY DIFFRACTION

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

Tumor necrosis factor ligand superfamily member 9

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor receptor superfamily member 9 × 1 （Q07011） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TNFL9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–197； UniProt 58–254 Author chain C； PDBConstruct 1–197； UniProt 58–254 Author chain E； PDBConstruct 1–197； UniProt 58–254 Author chain G； PDBConstruct 1–197； UniProt 58–254 Author chain I； PDBConstruct 1–197； UniProt 58–254 Author chain K； PDBConstruct 1–197； UniProt 58–254 Author chain M； PDBConstruct 1–197； UniProt 58–254 Author chain O； PDBConstruct 1–197； UniProt 58–254 Author chain Q； PDBConstruct 1–197； UniProt 58–254 Author chain S； PDBConstruct 1–197； UniProt 58–254 Author chain U； PDBConstruct 1–197； UniProt 58–254 Author chain W； PDBConstruct 1–197； UniProt 58–254

Tumor necrosis factor receptor superfamily member 9

Homo sapiens

UniProt Q07011

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	Tumor necrosis factor ligand superfamily member 9 × 1 （P41273） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TNR9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–157； UniProt 24–180 Author chain D； PDBConstruct 1–157； UniProt 24–180 Author chain F； PDBConstruct 1–157； UniProt 24–180 Author chain H； PDBConstruct 1–157； UniProt 24–180 Author chain J； PDBConstruct 1–157； UniProt 24–180 Author chain L； PDBConstruct 1–157； UniProt 24–180 Author chain N； PDBConstruct 1–157； UniProt 24–180 Author chain P； PDBConstruct 1–157； UniProt 24–180 Author chain R； PDBConstruct 1–157； UniProt 24–180 Author chain T； PDBConstruct 1–157； UniProt 24–180 Author chain V； PDBConstruct 1–157； UniProt 24–180 Author chain X； PDBConstruct 1–157； UniProt 24–180

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	6a3v
Deposition date deposition_date	2018-06-17
Structure title title	Complex structure of human 4-1BB and 4-1BBL
Keywords keywords	complex structure, agonist monoclonal antibody, cross-linking, IMMUNE SYSTEM; 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.

6a3v__assembly_9__model_1

Assembly 9 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6a3v__assembly_9__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6a3v__assembly_9__model_1 | P(r) · Pending

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

Rg（Guinier）	24.83 Å
Rg (electron density)	25.01 Å
Total Rg	25.56 Å
Atom count	1988
Residues	266
Excluded volume	35083 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6a3v__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6a3v__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6a3v__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6a3v__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6a3v__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6a3v__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`6a3v__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`6a3v__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`6a3v__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`6a3v__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`6a3v__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`6a3v__assembly_12__model_1`	dimeric （2）	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	Tumor necrosis factor ligand superfamily member 9
Molecular weight formula_weight	21517.3 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O,Q,S,U,W
Atom count atom_count	25073

ARASPGSAASPRLREGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Baculovirus transfer vector pFASTBAC1

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 9
Molecular weight formula_weight	17523.7 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P,R,T,V,X

LQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQDCKQGQELTKKGCKDCCFGTFNDQKRGICRPWTNCSLDGKSVLVNGTKERDVVCGPSPADLSPGASSVTPPAPAREHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Baculovirus transfer vector pFASTBAC1

Entity 3 Entity 3 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	12

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6. Fold Classification (SCOP + CATH) 23 domains

CATH v4.4 (23 domains)

Domain ID domain_id	6a3vA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vB02
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	6a3vC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vD02
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	6a3vE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vF02
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	6a3vG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vH02
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	6a3vI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vJ02
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	6a3vK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vL02
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	6a3vM00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vN02
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	6a3vO00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vP02
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	6a3vQ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vS00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vT02
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	6a3vU00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vV02
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	6a3vW00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6a3vX02
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	126.091 Å
Unit-cell length b length_b	137.195 Å
Unit-cell length c length_c	140.318 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.391 Å
Low-resolution limit resolution_low	44.666 Å
R factor r_factor	0.2650
R_work r_work	0.2635
R_free r_free	0.2930

Complex structure of human 4-1BB and 4-1BBL

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

Tumor necrosis factor ligand superfamily member 9

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor receptor superfamily member 9

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

6a3v__assembly_9__model_1

6a3v__assembly_9__model_1 | I(q)

6a3v__assembly_9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 23 domains

CATH v4.4 (23 domains)

7. Citations (1)

Complex structure of human 4-1BB and 4-1BBL

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

Tumor necrosis factor ligand superfamily member 9

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 receptor superfamily member 9

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

6a3v__assembly_9__model_1

6a3v__assembly_9__model_1 | I(q)

6a3v__assembly_9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 23 domains

CATH v4.4 (23 domains)

7. Citations (1)