6cpr

Crystal structure of 4-1BBL/4-1BB complex in C2 space group

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 6	Tumor necrosis factor receptor superfamily member 9 × 3 （Q07011） GLYCEROL × 1 CHLORIDE ION × 7 SULFATE ION × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SODIUM ION × 2 water × 6	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 1–165； UniProt 80–244 Author chain B； PDBConstruct 1–165； UniProt 80–244 Author chain C； PDBConstruct 1–165； UniProt 80–244

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 6	Tumor necrosis factor ligand superfamily member 9 × 3 （P41273） GLYCEROL × 1 CHLORIDE ION × 7 SULFATE ION × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SODIUM ION × 2 water × 6	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 D； PDBConstruct 1–138； UniProt 23–160 Author chain E； PDBConstruct 1–138； UniProt 23–160 Author chain F； PDBConstruct 1–138； UniProt 23–160

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	6cpr
Deposition date deposition_date	2018-03-14
Structure title title	Crystal structure of 4-1BBL/4-1BB complex in C2 space group
Keywords keywords	complex, CYTOKINE; CYTOKINE
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.

6cpr__assembly_1__model_1

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

Download this curve (.dat)

6cpr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cpr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.28 Å
Rg (electron density)	30.94 Å
Total Rg	31.57 Å
Atom count	6109
Residues	848
Excluded volume	106850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cpr__assembly_1__model_1`	hexameric （6）	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 (8)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor ligand superfamily member 9
Molecular weight formula_weight	17488.9 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	6257

DPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEI

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Insect cell expression vector pTIE1

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 9
Molecular weight formula_weight	14891.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

SLQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDICRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQDCKQGQELTKKGCKDCCFGTFNDQKRGICRPWTNCSLDGKSVLVNGTKERDVVCGP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Insect cell expression vector pTIE1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 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	3

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6cprA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6cprB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6cprC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6cprD02
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	6cprE02
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	6cprF02
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	115.280 Å
Unit-cell length b length_b	66.504 Å
Unit-cell length c length_c	129.356 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	38.000 Å
R factor r_factor	0.2503
R_work r_work	0.2487
R_free r_free	0.2796

Crystal structure of 4-1BBL/4-1BB complex in C2 space group

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

6cpr__assembly_1__model_1

6cpr__assembly_1__model_1 | I(q)

6cpr__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of 4-1BBL/4-1BB complex in C2 space group

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

6cpr__assembly_1__model_1

6cpr__assembly_1__model_1 | I(q)

6cpr__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)