SAXSdb — 2vj0

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 693–938	Fragment：APPENDAGE DOMAIN, RESIDUES 693-938	SYNAPTOJANIN-1 × 1 （O43426） AMPHIPHYSIN × 1 （O08838） BEN BENZAMIDINE × 1 DTD DITHIANE DIOL × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；1.2M AMMONIUM SULPHATE, 3% ISOPROPANOL AND 0.05M SODIUM CITRATE PH 6.5	Resolution 1.60 Å R-free 0.208

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 2VJ0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B9K ALPHA-ADAPTIN APPENDAGE DOMAIN, FROM CLATHRIN ADAPTOR AP2 Deposited 1999-02-11	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 701–938（238 aa） Fragment：APPENDAGE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；20% PEG 4000, 10% ISOPROPANOL, 100MM NA CITRATE PH 6.0, 10MM DTT, 6MG/ML PROTEIN	Resolution 1.90 Å R-free 0.221
1KY6 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW PEPTIDE Deposited 2002-02-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 701–938（238 aa） Fragment：C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.245
1KY7 THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH AMPHIPHYSIN FXDXF Deposited 2002-02-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 701–938（238 aa） Fragment：C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å R-free 0.252
1KYD AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW PEPTIDE Deposited 2002-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 701–938（238 aa） Fragment：C-TERMINAL APPENDAGE (EAR), RESIDUES 701-938	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.228
1KYF AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF PEPTIDE Deposited 2002-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 701–938（238 aa） Fragment：C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.22 Å R-free 0.211
1KYU AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF PEPTIDE Deposited 2002-02-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 701–938（238 aa） Fragment：C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.223
1QTP CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE Deposited 1999-06-28	Different construct Different mutation/modification 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 692–938（247 aa） Fragment：C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938	Mutation：SELENOMETHIONINE SUBSTITUTED PROTEIN Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；1.5 M MAGNESIUM SULFATE, 100 MM MES, 10MM SPERMINE TETRA-HCL, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.211
1QTS CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE Deposited 1999-06-29	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 692–938（247 aa） Fragment：C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；1.3 M AMMONIUM SULFATE, 80 MM HEPES, 8% DIOXANE, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.209
1W80 Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170 Deposited 2004-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 695–938（244 aa） Fragment：APPENDAGE DOMAIN, RESIDUES 695-938	Not recorded	BEN BENZAMIDINE × 1 CO3 CARBONATE ION × 3 DTD DITHIANE DIOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.2M AMMONIUM SULFATE, 3% ISOPROPANOL, 0.05M SODIUM CITRATE, pH 6.50	Resolution 1.90 Å R-free 0.224
2JKR AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE Deposited 2008-08-29	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 A 1–271（271 aa） Fragment：ALPHA CHAIN, RESIDUES 1-620 Chain A 272–620（349 aa） Fragment：ALPHA CHAIN, RESIDUES 1-620	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 1–271（271 aa） Fragment：ALPHA CHAIN, RESIDUES 1-620 Chain L 272–620（349 aa） Fragment：ALPHA CHAIN, RESIDUES 1-620	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 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 A 1–271（271 aa） Fragment：ALPHA CHAIN, RESIDUES 1-620 Chain A 272–620（349 aa） Fragment：ALPHA CHAIN, RESIDUES 1-620	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 1–271（271 aa） Fragment：ALPHA CHAIN, RESIDUES 1-620 Chain L 272–620（349 aa） Fragment：ALPHA CHAIN, RESIDUES 1-620	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
7OHI FCHO1-peptide-AP2 alpha ear complex Deposited 2021-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 695–938（244 aa）	Not recorded	SO4 SULFATE ION × 5 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.6M Magnesium sulfate heptahydrate 0.1M MES pH 6.5. The crystal were subsequently cryo-protected with ~20% glycerol final.	Resolution 1.41 Å R-free 0.215
7RW8 AP2 bound to heparin in the closed conformation Deposited 2021-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–620（620 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot force -10, 4 second blot, 4 uL sample	Resolution 3.50 Å
7RW9 AP2 bound to heparin in the bowl conformation Deposited 2021-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–620（620 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot force -10, 4 second blot, 4 uL sample	Resolution 3.90 Å
7RWA AP2 bound to heparin and Tgn38 tyrosine cargo peptide Deposited 2021-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–620（620 aa） Chain a 1–620（620 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot force -10, 4 second blot, 4 uL sample	Resolution 4.70 Å
7RWB AP2 bound to the APA domain of SGIP in the presence of heparin Deposited 2021-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–620（620 aa） Chain a 1–620（620 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot force -10, 4 second blot, 4 uL sample	Resolution 3.90 Å
7RWC AP2 bound to the APA domain of SGIP and heparin; partial signal subtraction and symmetry expansion Deposited 2021-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–620（620 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot force -10, 4 second blot, 4 uL sample	Resolution 3.80 Å
8T1O AP2 bound to MSP2N2 nanodisc with Tgn38 cargo peptide; composite map Deposited 2023-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–620（620 aa）	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 100 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Two applications of sample.	Resolution 3.30 Å
9PPP Structure of Alpha Appendage of AP2 bound to the extended FxDxF motif derived of CCDC32 Deposited 2025-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 695–938（244 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM SPG pH 8.0, 25% PEG 1500	Resolution 2.10 Å R-free 0.205
9PPP Structure of Alpha Appendage of AP2 bound to the extended FxDxF motif derived of CCDC32 Deposited 2025-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 695–938（244 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM SPG pH 8.0, 25% PEG 1500	Resolution 2.10 Å R-free 0.205
9PUE Structure of Alpha Appendage of AP2 bound to the FxDxF motif derived of CCDC32 Deposited 2025-07-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 695–938（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；40% isopropanol, 100 mM imidazole pH 6.5, 15% PEG 8000	Resolution 1.91 Å R-free 0.230
9PWA Closed AP-2 clathrin adaptor complex in solution Deposited 2025-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–620（620 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.55 Å
9PWB Structure of AP-2 bound to the dileucine motif of CCDC32; combined map Deposited 2025-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 9–620（612 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.64 Å
9PWC Composite structure of AP-2 bound to the dileucine motif and WxxPhi motif of CCDC32 Deposited 2025-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–620（620 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.00 Å

23 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AP2A2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–250； UniProt 693–938

SYNAPTOJANIN-1

OrganismNot specified

UniProt O43426

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 1479–1490	Fragment：PEPTIDE CONTAINING WVXF MOTIF, RESIDUES 1479-1490	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AMPHIPHYSIN × 1 （O08838） BEN BENZAMIDINE × 1 DTD DITHIANE DIOL × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；1.2M AMMONIUM SULPHATE, 3% ISOPROPANOL AND 0.05M SODIUM CITRATE PH 6.5	Resolution 1.60 Å R-free 0.208

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 2VJ0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W80 Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170 Deposited 2004-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 1479–1490（12 aa） Fragment：PEPTIDE CONTAINING WVXF MOTIF, RESIDUES 1479-1490 Chain Q 1460–1471（12 aa） Fragment：PEPTIDE CONTAINING FXDXF MOTIF, RESIDUES 1460-1471	Not recorded	BEN BENZAMIDINE × 1 CO3 CARBONATE ION × 3 DTD DITHIANE DIOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.2M AMMONIUM SULFATE, 3% ISOPROPANOL, 0.05M SODIUM CITRATE, pH 6.50	Resolution 1.90 Å R-free 0.224
2DNR Solution structure of RNA binding domain in Synaptojanin 1 Deposited 2006-04-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 894–971（78 aa） Fragment：RNA recognition motif	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.11mM 13C-15N PROTEIN, 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
7A0V Crystal structure of the 5-phosphatase domain of Synaptojanin1 in complex with a nanobody Deposited 2020-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 528–873（346 aa） Chain C 528–873（346 aa） Chain E 528–873（346 aa）	Not recorded	PO4 PHOSPHATE ION × 3 MG MAGNESIUM ION × 3 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；15% PEG 4000, 0.1 M sodium citrate pH 5, 10% 2-propanol	Resolution 2.30 Å R-free 0.252
7A17 Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody Deposited 2020-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 528–873（346 aa）	Not recorded	IP9 (2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；15% PEG 3350, 0.1 M sodium citrate pH 5.5, 13% ethanol	Resolution 2.73 Å R-free 0.257
7A17 Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody Deposited 2020-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 529–873（345 aa）	Not recorded	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；15% PEG 3350, 0.1 M sodium citrate pH 5.5, 13% ethanol	Resolution 2.73 Å R-free 0.257
7A17 Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody Deposited 2020-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 529–873（345 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；15% PEG 3350, 0.1 M sodium citrate pH 5.5, 13% ethanol	Resolution 2.73 Å R-free 0.257

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYNJ1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–12； UniProt 1479–1490

AMPHIPHYSIN

OrganismNot specified

UniProt O08838

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain Q； UniProt 324–330	Fragment：PEPTIDE CONTAINING FXDNF MOTIF, RESIDUES 324-330	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） SYNAPTOJANIN-1 × 1 （O43426） BEN BENZAMIDINE × 1 DTD DITHIANE DIOL × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；1.2M AMMONIUM SULPHATE, 3% ISOPROPANOL AND 0.05M SODIUM CITRATE PH 6.5	Resolution 1.60 Å R-free 0.208

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 2VJ0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5M5T Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (Amph4T1) Deposited 2016-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 349–358（10 aa） Fragment：UNP residues 349-358 Chain G 349–358（10 aa） Fragment：UNP residues 349-358 Chain I 349–358（10 aa） Fragment：UNP residues 349-358	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 1 uL reservoir equilibrated against a 200 uL reservoir of 1.1 M sodium malonate pH 8.0	Resolution 1.70 Å R-free 0.185
5M5T Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (Amph4T1) Deposited 2016-10-22	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 F 349–358（10 aa） Fragment：UNP residues 349-358 Chain H 349–358（10 aa） Fragment：UNP residues 349-358 Chain J 349–358（10 aa） Fragment：UNP residues 349-358	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 1 uL reservoir equilibrated against a 200 uL reservoir of 1.1 M sodium malonate pH 8.0	Resolution 1.70 Å R-free 0.185

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMPH_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Q； PDBConstruct 1–7； UniProt 324–330

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	2vj0
Deposition date deposition_date	2007-12-06
Structure title title	Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170
Keywords keywords	;PROTEIN TRANSPORT, CYTOPLASMIC VESICLE, ALTERNATIVE SPLICING, TRANSPORT, COATED PIT, SH3 DOMAIN, ENDOCYTOSIS, ALPHA-ADAPTIN, GOLGI APPARATUS, PHOSPHORYLATION, AP2, SYNAPSE, MEMBRANE, CYTOPLASM, COILED COIL, AMPHIPHYSIN, CYTOSKELETON, SYNAPTOJANIN, LIPID-BINDING, CELL JUNCTION ;; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.35 Å
Radius of gyration Rg (electron density) rg_electron	20.41 Å
Forward intensity I(0) i0	15735900.00
Molecular weight molecular_weight	29926.0 kDa
Excluded volume excluded_volume	37483 Å³
Envelope volume envelope_volume	43704 Å³
Hydration-shell volume shell_volume	18647 Å³
Envelope diameter envelope_diameter	70.9 Å
Shell Rg shell_rg	26.07 Å
Envelope Rg envelope_rg	20.65 Å
Shape Rg shape_rg	20.43 Å
Total Rg total_rg	21.16 Å
Total atoms total_atoms	2101
Residues n_residues	261
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.5 Å
Rg (real space) rg_real	21.43 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.5740e+07
I(0) uncertainty (real space) i0_real_error	2.2380e+05
Rg (reciprocal space) rg_reciprocal	21.41 Å
I(0) (reciprocal space) i0_reciprocal	15740000.0000
Solution quality estimate total_estimate	0.8716
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.472
Kurtosis Kurtosis kurtosis	-0.201
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3313000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	AP-2 COMPLEX SUBUNIT ALPHA-2
Molecular weight formula_weight	28048.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2463

GSPGILAPLAPGSEDNFARFVCKNNGVLFENQLLQIGLKSEFRQNLGRMFIFYGNKTSTQFLNFTPTLICADDLQTNLNLQTKPVDPTVDGGAQVQQVINIECISDFTEAPVLNIQFRYGGTFQNVSVKLPITLNKFFQPTEMASQDFFQRWKQLSNPQQEVQNIFKAKHPMDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQMYRLTLRTSKDTVSQRLCELLSEQF

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	SYNAPTOJANIN-1
Molecular weight formula_weight	1465.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

NPKGWVTFEEEE

Entity 3 Entity 3 polymer

Description description	AMPHIPHYSIN
Molecular weight formula_weight	866.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

FEDNFVP

Entity 4 Entity 4 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	DITHIANE DIOL
Molecular weight formula_weight	152.2 kDa
Source method src_method	syn
Copy count entity_count	1

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	3

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vj0a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.10 — Clathrin adaptor appendage domain
Family Family family	b.1.10.1 — Alpha-adaptin ear subdomain-like

Domain ID domain_id	d2vj0a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.105 — Subdomain of clathrin and coatomer appendage domain
Superfamily Superfamily superfamily	d.105.1 — Subdomain of clathrin and coatomer appendage domain
Family Family family	d.105.1.1 — Clathrin adaptor appendage, alpha and beta chain-specific domain

CATH v4.4 (2 domains)

Domain ID domain_id	2vj0A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1230 — Gamma-adaptin ear (GAE) domain

Domain ID domain_id	2vj0A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

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8. Citations (1)

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Unit-cell length a length_a	144.508 Å
Unit-cell length b length_b	66.980 Å
Unit-cell length c length_c	39.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	17.760 Å
R factor r_factor	0.1820
R_work r_work	0.1810
R_free r_free	0.2080

fit	/app/data/saxs_computation/vj/2vj0/2vj0.fit
pddf	/app/data/pr_computation/vj/2vj0/2vj0.pr.out
profile	/app/data/saxs_computation/vj/2vj0/2vj0.dat

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170

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

SYNAPTOJANIN-1

State in the Current Structure

Other States of the Same Protein in the Database

AMPHIPHYSIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)