2jkr

AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE

Method: X-RAY DIFFRACTION

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

AP-2 COMPLEX SUBUNIT ALPHA-2

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT BETA-1 × 1 （P63010） AP-2 COMPLEX SUBUNIT SIGMA-1 × 1 （P62743） AP-2 COMPLEX SUBUNIT MU-1 × 1 （P84092） CD4 PEPTIDE × 1 （B0AZV7） SULFATE ION × 14 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT BETA-1 × 1 （P63010） AP-2 COMPLEX SUBUNIT SIGMA-1 × 1 （P62743） AP-2 COMPLEX SUBUNIT MU-1 × 1 （P84092） CD4 PEPTIDE × 1 （B0AZV7） SULFATE ION × 17 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2A2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–271； UniProt 1–271 Author chain A； PDBConstruct 273–621； UniProt 272–620 Author chain L； PDBConstruct 1–271； UniProt 1–271 Author chain L； PDBConstruct 273–621； UniProt 272–620

AP-2 COMPLEX SUBUNIT BETA-1

HOMO SAPIENS

UniProt P63010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AP-2 COMPLEX SUBUNIT SIGMA-1 × 1 （P62743） AP-2 COMPLEX SUBUNIT MU-1 × 1 （P84092） CD4 PEPTIDE × 1 （B0AZV7） SULFATE ION × 14 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AP-2 COMPLEX SUBUNIT SIGMA-1 × 1 （P62743） AP-2 COMPLEX SUBUNIT MU-1 × 1 （P84092） CD4 PEPTIDE × 1 （B0AZV7） SULFATE ION × 17 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2B1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–591； UniProt 1–591 Author chain E； PDBConstruct 1–591； UniProt 1–591

AP-2 COMPLEX SUBUNIT SIGMA-1

MUS MUSCULUS

UniProt P62743

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AP-2 COMPLEX SUBUNIT BETA-1 × 1 （P63010） AP-2 COMPLEX SUBUNIT MU-1 × 1 （P84092） CD4 PEPTIDE × 1 （B0AZV7） SULFATE ION × 14 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AP-2 COMPLEX SUBUNIT BETA-1 × 1 （P63010） AP-2 COMPLEX SUBUNIT MU-1 × 1 （P84092） CD4 PEPTIDE × 1 （B0AZV7） SULFATE ION × 17 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2S1_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–142； UniProt 1–142 Author chain S； PDBConstruct 1–142； UniProt 1–142

AP-2 COMPLEX SUBUNIT MU-1

RATTUS NORVEGICUS

UniProt P84092

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AP-2 COMPLEX SUBUNIT BETA-1 × 1 （P63010） AP-2 COMPLEX SUBUNIT SIGMA-1 × 1 （P62743） CD4 PEPTIDE × 1 （B0AZV7） SULFATE ION × 14 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AP-2 COMPLEX SUBUNIT BETA-1 × 1 （P63010） AP-2 COMPLEX SUBUNIT SIGMA-1 × 1 （P62743） CD4 PEPTIDE × 1 （B0AZV7） SULFATE ION × 17 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2M1_RAT
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain M； PDBConstruct 1–435； UniProt 1–435 Author chain U； PDBConstruct 1–435； UniProt 1–435

CD4 PEPTIDE

OrganismNot specified

UniProt B0AZV7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AP-2 COMPLEX SUBUNIT BETA-1 × 1 （P63010） AP-2 COMPLEX SUBUNIT SIGMA-1 × 1 （P62743） AP-2 COMPLEX SUBUNIT MU-1 × 1 （P84092） SULFATE ION × 14 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AP-2 COMPLEX SUBUNIT BETA-1 × 1 （P63010） AP-2 COMPLEX SUBUNIT SIGMA-1 × 1 （P62743） AP-2 COMPLEX SUBUNIT MU-1 × 1 （P84092） SULFATE ION × 17 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B0AZV7_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain P； PDBConstruct 1–11； UniProt 252–262 Author chain Q； PDBConstruct 1–11； UniProt 252–262

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	2jkr
Deposition date deposition_date	2008-08-29
Structure title title	AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE
Keywords keywords	;ALTERNATIVE SPLICING, PHOSPHOPROTEIN, PHOSPHORYLATION, PROTEIN TRANSPORT, ADAPTOR, MEMBRANE, TRANSPORT, COATED PIT, ENDOCYTOSIS, CELL MEMBRANE, LIPID-BINDING ;; ENDOCYTOSIS
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.

2jkr__assembly_1__model_1

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

Download this curve (.dat)

2jkr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jkr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.00 Å
Rg (electron density)	39.23 Å
Total Rg	39.72 Å
Atom count	14043
Residues	1751
Excluded volume	252520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jkr__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2jkr__assembly_2__model_1`	pentameric （5）	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 (7)

Entity 1 Entity 1 polymer

Description description	AP-2 COMPLEX SUBUNIT ALPHA-2
Molecular weight formula_weight	69786.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,L
Atom count atom_count	28120

MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVCKLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDLASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSPDLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSASTDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKVQHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSIREEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAAKTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRALLLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLEEMPPFPERESSILAKLKKKKGGS

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	AP-2 COMPLEX SUBUNIT BETA-1
Molecular weight formula_weight	66953.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

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	AP-2 COMPLEX SUBUNIT SIGMA-1
Molecular weight formula_weight	17038.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,S

MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 polymer

Description description	AP-2 COMPLEX SUBUNIT MU-1
Molecular weight formula_weight	49726.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,U

MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYETRC

Source Source

Source organism organism	RATTUS NORVEGICUS
Common name common_name	RAT
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	ESCHERICHIA COLI

Entity 5 Entity 5 polymer

Description description	CD4 PEPTIDE
Molecular weight formula_weight	1443.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

RMSQIKRLLSE

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	31

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2jkrb_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.10 — Clathrin adaptor core protein

Domain ID domain_id	d2jkre_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.10 — Clathrin adaptor core protein

Domain ID domain_id	d2jkri_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.4 — SNARE-like
Family Family family	d.110.4.2 — Clathrin coat assembly domain

Domain ID domain_id	d2jkrs_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.4 — SNARE-like
Family Family family	d.110.4.2 — Clathrin coat assembly domain

CATH v4.4 (12 domains)

Domain ID domain_id	2jkrA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	2jkrB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	2jkrE00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	2jkrI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2jkrL01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	2jkrM01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2jkrM02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1170 — Mu homology domain, subdomain B

Domain ID domain_id	2jkrM03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1170 — Mu homology domain, subdomain B

Domain ID domain_id	2jkrS00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2jkrU01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2jkrU02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1170 — Mu homology domain, subdomain B

Domain ID domain_id	2jkrU03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1170 — Mu homology domain, subdomain B

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Unit-cell length a length_a	169.900 Å
Unit-cell length b length_b	169.900 Å
Unit-cell length c length_c	321.700 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.980 Å
Low-resolution limit resolution_low	50.950 Å
R factor r_factor	0.2020
R_work r_work	0.1990
R_free r_free	0.2600

AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE

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

AP-2 COMPLEX SUBUNIT ALPHA-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-2 COMPLEX SUBUNIT BETA-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-2 COMPLEX SUBUNIT SIGMA-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-2 COMPLEX SUBUNIT MU-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CD4 PEPTIDE

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

2jkr__assembly_1__model_1

2jkr__assembly_1__model_1 | I(q)

2jkr__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 (7)

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 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)