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1i31

MU2 ADAPTIN SUBUNIT (AP50) OF AP2 CLATHRIN ADAPTOR, COMPLEXED WITH EGFR INTERNALIZATION PEPTIDE FYRALM AT 2.5 A RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 88.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CLATHRIN COAT ASSEMBLY PROTEIN AP50

Rattus norvegicus

UniProt P84092

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 122–435 Fragment：RESIDUES 122-435 EPIDERMAL GROWTH FACTOR RECEPTOR × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；SODIUM FORMATE, SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.50 Å R-free 0.255

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1I31 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BW8 MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH EGFR INTERNALIZATION PEPTIDE FYRALM Deposited 1998-09-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 122–435（314 aa） Fragment：INTERNALIZATION SIGNAL BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1, vapor diffusion - hanging drop
Resolution 2.65 Å R-free 0.296
1BXX MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH TGN38 INTERNALIZATION PEPTIDE DYQRLN Deposited 1998-10-08 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–435（278 aa） Fragment：INTERNALIZATION SIGNAL BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；289 K；HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1, vapor diffusion - hanging drop, temperature 289K
Resolution 2.70 Å R-free 0.325
2BP5 MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH NON-CANONICAL INTERNALIZATION PEPTIDE VEDYEQGLSG Deposited 2005-04-18 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 1–435（435 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；289 K；2.2M NACL, 0.4M NA/K PHOSPHATE PH 7.1, 10MM DTT, 0.1M MES, 15% GLYCEROL, 16 DEGREES
Resolution 2.80 Å R-free 0.251
2JKR AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE Deposited 2008-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 1–435（435 aa）
Not recorded SO4 SULFATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.7-2.2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH6 .5 AND 5MM DTT FROM A MIXTURE OF 10MG/ML AP2 CORE AND 7MG/ML PEPTIDE. CRYOPROTECTED WITH 1.8-2.3M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 6.5, 17% GLYCEROL AND 7MG/ ML CD4 DILEUCINE PEPTIDE
Resolution 2.98 Å R-free 0.260
2JKR AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE Deposited 2008-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain U 1–435（435 aa）
Not recorded SO4 SULFATE ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.7-2.2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH6 .5 AND 5MM DTT FROM A MIXTURE OF 10MG/ML AP2 CORE AND 7MG/ML PEPTIDE. CRYOPROTECTED WITH 1.8-2.3M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 6.5, 17% GLYCEROL AND 7MG/ ML CD4 DILEUCINE PEPTIDE
Resolution 2.98 Å R-free 0.260
2JKT AP2 CLATHRIN ADAPTOR CORE with CD4 Dileucine peptide RM(phosphoS) EIKRLLSE Q to E mutant Deposited 2008-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 1–435（435 aa）
Not recorded SO4 SULFATE ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.7-2.2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH6 .5 AND 5MM DTT FROM A MIXTURE OF 10MG/ML AP2 CORE AND 7MG/ML PEPTIDE. CRYOPROTECTED WITH 1.8-2.3M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 6.5, 17% GLYCEROL AND 7MG/ ML CD4 DILEUCINE PEPTIDE
Resolution 3.40 Å R-free 0.256
2JKT AP2 CLATHRIN ADAPTOR CORE with CD4 Dileucine peptide RM(phosphoS) EIKRLLSE Q to E mutant Deposited 2008-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain U 1–435（435 aa）
Not recorded SO4 SULFATE ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.7-2.2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH6 .5 AND 5MM DTT FROM A MIXTURE OF 10MG/ML AP2 CORE AND 7MG/ML PEPTIDE. CRYOPROTECTED WITH 1.8-2.3M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 6.5, 17% GLYCEROL AND 7MG/ ML CD4 DILEUCINE PEPTIDE
Resolution 3.40 Å R-free 0.256
2PR9 Mu2 adaptin subunit (AP50) of AP2 adaptor (second domain), complexed with GABAA receptor-gamma2 subunit-derived internalization peptide DEEYGYECL Deposited 2007-05-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–435（278 aa） Fragment：second domain (residues 158-435)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；2.0 M sodium formate, 0.1 M Na-acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.51 Å R-free 0.240
2VGL AP2 CLATHRIN ADAPTOR CORE Deposited 2007-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 1–435（435 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；18% PEG, 10MM NA/K PHOSPHATE PH 6.2, 200MM NACL, 4MM DTT, IP6
Resolution 2.60 Å R-free 0.339
2XA7 AP2 clathrin adaptor core in active complex with cargo peptides Deposited 2010-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 1–236（236 aa）
Chain M 237–435（199 aa）
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.6-0.8M LISO4, 0.6-0.7M NH4SO4, 100MM NA CITRATE PH 6.5; CRYOPROTECTANT 20% GLYCEROL
Resolution 3.10 Å R-free 0.285
2XA7 AP2 clathrin adaptor core in active complex with cargo peptides Deposited 2010-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 1–236（236 aa）
Chain M 237–435（199 aa）
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.6-0.8M LISO4, 0.6-0.7M NH4SO4, 100MM NA CITRATE PH 6.5; CRYOPROTECTANT 20% GLYCEROL
Resolution 3.10 Å R-free 0.285
3H85 Molecular basis for the association of PIPKI gamma-p90 with the clathrin adaptor AP-2 Deposited 2009-04-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–435（278 aa） Fragment：UNP residues 158-435
Not recorded NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.4M sodium formate, 50mM NiCl, 0.1M Na-acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 2.60 Å R-free 0.263
3ML6 a complex between Dishevelled2 and clathrin adaptor AP-2 Deposited 2010-04-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 170–435（266 aa） Fragment：PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.335
3ML6 a complex between Dishevelled2 and clathrin adaptor AP-2 Deposited 2010-04-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 170–435（266 aa） Fragment：PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.335
3ML6 a complex between Dishevelled2 and clathrin adaptor AP-2 Deposited 2010-04-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 170–435（266 aa） Fragment：PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.335
3ML6 a complex between Dishevelled2 and clathrin adaptor AP-2 Deposited 2010-04-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 170–435（266 aa） Fragment：PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.335
3ML6 a complex between Dishevelled2 and clathrin adaptor AP-2 Deposited 2010-04-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain E 170–435（266 aa） Fragment：PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.335
3ML6 a complex between Dishevelled2 and clathrin adaptor AP-2 Deposited 2010-04-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain F 170–435（266 aa） Fragment：PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.335
4UQI AP2 controls clathrin polymerization with a membrane-activated switch Deposited 2014-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 1–435（435 aa）
Not recorded CL CHLORIDE ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；18% PEG1000, 10MM NA/K PHOSPHATE PH 6.2, 200MM NACL, 4MM DTT, IP6
Resolution 2.79 Å R-free 0.259
5C7Z AP2 Mu2 adaptin C-terminal domain complexed with integrin alpha-4 peptide Deposited 2015-06-25 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 159–435（277 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293 K；2.2M NaCl, 0.4M Na/K phosphate, 10MM DTT 0.1M MES pH 7.1, 15% glycerol, molar ratio of peptide to protein 3:1
Resolution 2.77 Å R-free 0.224
5FPI Mu2 adaptin subunit of the AP2 adaptor (C-terminal domain) complexed with Integrin alpha4 internalisation peptide QYKSILQE Deposited 2015-11-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–435（435 aa） Fragment：INTERNALISATION SIGNAL BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；2.2M NACL, 0.4M NAKPHOSPHATE, 20% V/V GLYCEROL, 0.1M MES PH6.5, 5MM DTT
Resolution 2.77 Å R-free 0.224
5WRK Mu2 subunit of the clathrin adaptor complex AP2 in complex with IRS-1 Y608 peptide Deposited 2016-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–223（66 aa） Fragment：UNP residues 158-223,UNP residues 261-435
Chain A 261–435（175 aa） Fragment：UNP residues 158-223,UNP residues 261-435
Not recorded NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.4M Na formate, 0.05M NiCl, 0.1M Na acetate pH 6.0
Resolution 2.62 Å R-free 0.223
5WRL Mu2 subunit of the clathrin adaptor complex AP2 in complex with IRS-1 Y628 peptide Deposited 2016-12-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–435（278 aa） Fragment：UNP residues 158-435
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；2.2M NaCl, 0.4M Na/K Phosphate, 0.01M DTT, 15% Glycerol, 0.1M MES pH 6.5
Resolution 3.10 Å R-free 0.251
5WRM Mu2 subunit of the clathrin adaptor complex AP2 in complex with IRS-1 Y658 peptide Deposited 2016-12-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–435（278 aa） Fragment：UNP residues 158-435
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；2.3M NaCl, 0.4M Na/K Phosphate, 0.01M DTT, 15% Glycerol, 0.1M MES pH 6.5
Resolution 2.60 Å R-free 0.227
6QH5 AP2 clathrin adaptor mu2T156-phosphorylated core in closed conformation Deposited 2019-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 1–435（435 aa）
Chain N 1–435（435 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；289 K；20% PEG 1000; 100 mM Na+/K+ phosphate buffer (pH 7.2), 200 mM NaCl, and 10 mM DTT
Resolution 2.56 Å R-free 0.257
6QH6 AP2 clathrin adaptor core with two cargo peptides in open+ conformation Deposited 2019-01-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain N 1–435（435 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；289 K；7.5% PVA, 9% 1-propanol, 90 mM Hepes pH 7.4, 100 mM guanidine hydrochloride
Resolution 5.00 Å R-free 0.285
6RH6 Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of NECAP1 PHear domain with phosphorylated AP2 mu2 148-163 Deposited 2019-04-18 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 149–163（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 70；Pressure 1
NMR sample composition 0.5 mM [U-98% 13C; U-98% 15N] NECAP1 1-133, 0.5 mM AP2 mu2 148-163, 70 mM [U-2H] sodium acetate, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM [U-98% 13C; U-98% 15N] NECAP1, 0.5 mM [U-98% 13C; U-98% 15N] AP2 mu2 148-163, 70 mM [U-2H] sodium acetate, 100% D2O | 100% D2O
Resolution not provided
6YAE AP2 core in physiological buffer Deposited 2020-03-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 1–435（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YAF AP2 on a membrane containing tyrosine-based cargo peptide Deposited 2020-03-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 1–435（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；The sample was supplemented with 10 nm nanogold fiducials, and 3 ul of the mixture was backside blotted for 3 seconds.
Resolution 9.10 Å
6YAH AP2 in clathrin coats assembled on a membrane containing dileucine- and tyrosine-based cargo peptides Deposited 2020-03-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 1–435（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；The sample was supplemented with 10 nm nanogold fiducials, and 3 ul of the mixture was backside blotted for 3 seconds.
Resolution 10.20 Å
7OFP Apo Structure of Mu2 Adaptin Subunit (Ap50) Of AP2 Clathrin Adaptor Deposited 2021-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 158–435（278 aa）
Not recorded GOL GLYCEROL × 6 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Protein (10 mg/ml) and peptide (DVDEEGYSIKPETNQNDTKENHFYSS) (2mg/ml) were equilibrated against 1.5M Ammonium Sulphate 0.1M Hepes pH 7.0. Crystals were cryo-protected by soaking in mother liquor supplemented with 20% glycerol and peptide (peptide did not crystallise).
Resolution 1.92 Å R-free 0.210
7OFP Apo Structure of Mu2 Adaptin Subunit (Ap50) Of AP2 Clathrin Adaptor Deposited 2021-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 158–435（278 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；Protein (10 mg/ml) and peptide (DVDEEGYSIKPETNQNDTKENHFYSS) (2mg/ml) were equilibrated against 1.5M Ammonium Sulphate 0.1M Hepes pH 7.0. Crystals were cryo-protected by soaking in mother liquor supplemented with 20% glycerol and peptide (peptide did not crystallise).
Resolution 1.92 Å R-free 0.210
7OG1 AP2 clathrin adaptor core in complex with cargo peptide and FCHO2 Deposited 2021-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain CCC 1–435（435 aa）
Chain MMM 1–435（435 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；Crystals of AP-2 in complex with FCHO2 linker and TGN38 peptide, supplemented with 10mM K Na Tartrate, grew in sitting drops with reservoir 0.1M Mg formate dehydrate, 10% to 15% PEG 3350. The crystals were cryo-protected with 0.1M Mg formate dehydrate, 13% PEG 3350, 18-24% Glycerol and 1mg/ml of peptide.
Resolution 3.25 Å R-free 0.306
7OHO Crystal structure of AP2 FCHO2 chimera Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain MMM 1–435（435 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；289 K；18% PEG 12000 0.1M Na/K phosphate pH 6.2 0.2M NaCl 4mM DTT in the presence of 3-fold molar excess of IP6.
Resolution 2.88 Å R-free 0.273
7OHZ Crystal structure of AP2 Mu2 - FCHO2 chimera (His6-tagged) Deposited 2021-05-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: trimeric
Chain B 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；20% w/v PEG 3,350 0.2 M DL-Malic acid pH 7.0. The crystals were cryo-protected by soaking in mother liquor supplemented with 30-32% glycerol.
Resolution 2.27 Å R-free 0.314
7OHZ Crystal structure of AP2 Mu2 - FCHO2 chimera (His6-tagged) Deposited 2021-05-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: trimeric
Chain A 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；20% w/v PEG 3,350 0.2 M DL-Malic acid pH 7.0. The crystals were cryo-protected by soaking in mother liquor supplemented with 30-32% glycerol.
Resolution 2.27 Å R-free 0.314
7OI5 Crystal structure of AP2 Mu2 - FCHO2 chimera (GST cleaved) Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 158–435（278 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；289 K；20% w/v PEG 3350, 0.2 M Sodium phosphate dibasic dehydrate pH 9.1. The crystal was cryo-protected by soaking in mother liquor supplemented with 25% glycerol.
Resolution 2.61 Å R-free 0.297
7OI5 Crystal structure of AP2 Mu2 - FCHO2 chimera (GST cleaved) Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 158–435（278 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；289 K；20% w/v PEG 3350, 0.2 M Sodium phosphate dibasic dehydrate pH 9.1. The crystal was cryo-protected by soaking in mother liquor supplemented with 25% glycerol.
Resolution 2.61 Å R-free 0.297
7OIQ Crystal structure of AP2 Mu2 in complex with FCHO2 WxxPhi motif (C2 crystal form) Deposited 2021-05-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain AAA 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；30mM Magnesium chloride hexahydrate, 30mM Calcium chloride dihydrate, 100mM Sodium HEPES MOPS (acid) pH 7.5, 20% v/v Ethylene glycol; 10 % w/v PEG 8000
Resolution 1.85 Å R-free 0.209
7OIQ Crystal structure of AP2 Mu2 in complex with FCHO2 WxxPhi motif (C2 crystal form) Deposited 2021-05-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain BBB 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；30mM Magnesium chloride hexahydrate, 30mM Calcium chloride dihydrate, 100mM Sodium HEPES MOPS (acid) pH 7.5, 20% v/v Ethylene glycol; 10 % w/v PEG 8000
Resolution 1.85 Å R-free 0.209
7Z5C Chimera of AP2 with FCHO2 linker domain as a fusion on Cmu2 subunit Deposited 2022-03-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 1–435（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50% HKT buffer (10mM Hepes, 10mM Tris 120mM potassium acetate pH 7.2) and 50% Core buffer (10mM Tris, 250mM NaCl, pH 8)
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
9FIW MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRHFA Deposited 2024-05-29 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol
Resolution 2.82 Å R-free 0.246
9FIX MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRPYSYRHFA Deposited 2024-05-29 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol
Resolution 2.78 Å R-free 0.233
9FIY MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRHFA Deposited 2024-05-29 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol
Resolution 2.88 Å R-free 0.242
9UUJ Crystal structure of the mu2 subunit of the clathrin-adaptor protein 2 (AP2) bound to HPV16 E7(residues 22-39) Deposited 2025-05-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2.0 M sodium formate and 100 mM sodium acetate trihydrate (pH 4.6)
Resolution 3.70 Å R-free 0.234
9UUK Crystal structure of the mu2 subunit of the clathrin-adaptor protein 2 (AP2) bound to HPV16 E7(residues 22-32; S31E and S32E) Deposited 2025-05-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2.5 M sodium chloride and 100 mM potassium phosphate monobasic/sodium phosphate dibasic (pH 6.2)
Resolution 3.20 Å R-free 0.244
9UUL Crystal structure of the mu2 subunit of the clathrin-adaptor protein 2 (AP2) bound to HPV16 E7(residues 22-39; S31E and S32E) Deposited 2025-05-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 158–435（278 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；3.5 M ammonium chloride and 100 mM sodium acetate trihydrate (pH 4.5)
Resolution 3.30 Å R-free 0.225

35 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AP2M1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–314； UniProt 122–435

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1i31

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1i31
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1i31
Deposition date deposition_date2001-02-12
Structure title titleMU2 ADAPTIN SUBUNIT (AP50) OF AP2 CLATHRIN ADAPTOR, COMPLEXED WITH EGFR INTERNALIZATION PEPTIDE FYRALM AT 2.5 A RESOLUTION
Keywords keywordsbeta-sandwich, peptide-binding site, protein-peptide complex, clathrin adaptor, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.22 Å
Radius of gyration Rg (electron density) rg_electron23.73 Å
Forward intensity I(0) i014811200.00
Molecular weight molecular_weight30244.0 kDa
Excluded volume excluded_volume38491 ų
Envelope volume envelope_volume47661 ų
Hydration-shell volume shell_volume18287 ų
Envelope diameter envelope_diameter88.6 Å
Shell Rg shell_rg28.72 Å
Envelope Rg envelope_rg24.27 Å
Shape Rg shape_rg23.72 Å
Total Rg total_rg24.47 Å
Total atoms total_atoms2122
Residues n_residues262
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax88.2 Å
Rg (real space) rg_real24.56 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real1.4810e+07
I(0) uncertainty (real space) i0_real_error2.1310e+05
Rg (reciprocal space) rg_reciprocal24.48 Å
I(0) (reciprocal space) i0_reciprocal14810000.0000
Solution quality estimate total_estimate0.7677
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.7 Å
Skewness Skewness skewness0.614
Kurtosis Kurtosis kurtosis-0.211
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5449000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.539; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.398; Smooth: 0.963
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1i31a_
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.7 — Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
Family Family familyb.2.7.1 — Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor

CATH v4.4 (2 domains)

Domain ID domain_id1i31A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1170 — Mu homology domain, subdomain B
Domain ID domain_id1i31A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1170 — Mu homology domain, subdomain B
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8. Citations (2)

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9. Files and Curves (10)