2z3r

Crystal structure of the IL-15/IL-15Ra complex

Method: X-RAY DIFFRACTION

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

Interleukin-15

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	Interleukin-15 receptor alpha chain × 1 （Q13261） GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 receptor alpha chain × 1 （Q13261） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 receptor alpha chain × 1 （Q13261） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 receptor alpha chain × 1 （Q13261） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 receptor alpha chain × 1 （Q13261） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 receptor alpha chain × 1 （Q13261） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 receptor alpha chain × 1 （Q13261） water × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 receptor alpha chain × 1 （Q13261） GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IL15_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–119； UniProt 49–162 Author chain C； PDBConstruct 6–119； UniProt 49–162 Author chain E； PDBConstruct 6–119； UniProt 49–162 Author chain G； PDBConstruct 6–119； UniProt 49–162 Author chain I； PDBConstruct 6–119； UniProt 49–162 Author chain K； PDBConstruct 6–119； UniProt 49–162 Author chain M； PDBConstruct 6–119； UniProt 49–162 Author chain O； PDBConstruct 6–119； UniProt 49–162

Interleukin-15 receptor alpha chain

Homo sapiens

UniProt Q13261

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 × 1 （P40933） GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 × 1 （P40933） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 × 1 （P40933） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 × 1 （P40933） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 × 1 （P40933） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 × 1 （P40933） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 × 1 （P40933） water × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Interleukin-15 × 1 （P40933） GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I15RA_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–107； UniProt 31–132 Author chain D； PDBConstruct 6–107； UniProt 31–132 Author chain F； PDBConstruct 6–107； UniProt 31–132 Author chain H； PDBConstruct 6–107； UniProt 31–132 Author chain J； PDBConstruct 6–107； UniProt 31–132 Author chain L； PDBConstruct 6–107； UniProt 31–132 Author chain N； PDBConstruct 6–107； UniProt 31–132 Author chain P； PDBConstruct 6–107； UniProt 31–132

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	2z3r
Deposition date deposition_date	2007-06-05
Structure title title	Crystal structure of the IL-15/IL-15Ra complex
Keywords keywords	Protein-Protein complex, CYTOKINE-CYTOKINE RECEPTOR COMPLEX; CYTOKINE/CYTOKINE RECEPTOR
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.

2z3r__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2z3r__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2z3r__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	19.25 Å
Rg (electron density)	18.44 Å
Total Rg	19.36 Å
Atom count	1496
Residues	191
Excluded volume	26757 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2z3r__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2z3r__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2z3r__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2z3r__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2z3r__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2z3r__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2z3r__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2z3r__assembly_8__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 (4)

Entity 1 Entity 1 polymer

Description description	Interleukin-15
Molecular weight formula_weight	13258.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	12517

AMAISNWVNVISDLKKIEDLIQSMHIDATLYTESDVHPSCKVTAMKCFLLELQVISLESGDASIHDTVENLIILANNSLSSNGNVTESGCKECEELEEKNIKEFLQSFVHIVQMFINTS

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	Interleukin-15 receptor alpha chain
Molecular weight formula_weight	11496.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

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

AMAISITCPPPMSVEHADIWVKSYSLYSRERYICNSGFKRKAGTSSLTECVLNKATNVAHWTTPSLKCIRDPALVHQRPAPPSTVTTAGVTPQPESLSPSGKEPAAS

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 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (32 domains)

Domain ID domain_id	d2z3ra2
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d2z3ra3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rb2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d2z3rb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rc2
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d2z3rc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rd2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d2z3rd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3re2
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d2z3re3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rf2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d2z3rf3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rg2
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d2z3rg3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rh2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d2z3rh3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3ri2
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d2z3ri3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rj2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d2z3rj3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rk2
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d2z3rk3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rl2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d2z3rl3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rm2
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d2z3rm3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rn2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d2z3rn3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3ro2
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d2z3ro3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2z3rp2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d2z3rp3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (16 domains)

Domain ID domain_id	2z3rA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2z3rB01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2z3rC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2z3rD01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2z3rE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2z3rF01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2z3rG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2z3rH01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2z3rI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2z3rJ01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2z3rK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2z3rL01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2z3rM00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2z3rN01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2z3rO00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	70 — Interleukin-15/Interleukin-21

Domain ID domain_id	2z3rP01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	230 —

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Unit-cell length a length_a	81.800 Å
Unit-cell length b length_b	127.035 Å
Unit-cell length c length_c	191.331 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.930 Å
R factor r_factor	0.2061
R_work r_work	0.2050
R_free r_free	0.2499

Crystal structure of the IL-15/IL-15Ra complex

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

Interleukin-15

State in the Current Structure

Other States of the Same Protein in the Database

Interleukin-15 receptor alpha chain

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

2z3r__assembly_6__model_1

2z3r__assembly_6__model_1 | I(q)

2z3r__assembly_6__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (32 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of the IL-15/IL-15Ra complex

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

Interleukin-15

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Interleukin-15 receptor alpha chain

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

2z3r__assembly_6__model_1

2z3r__assembly_6__model_1 | I(q)

2z3r__assembly_6__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (32 domains)

CATH v4.4 (16 domains)

7. Citations (1)