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- PDB-9ppp: Structure of Alpha Appendage of AP2 bound to the extended FxDxF m... -

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Basic information

Entry
Database: PDB / ID: 9ppp
TitleStructure of Alpha Appendage of AP2 bound to the extended FxDxF motif derived of CCDC32
Components
  • AP-2 complex subunit alpha-2
  • Coiled-coil domain-containing protein 32
KeywordsENDOCYTOSIS / Clathin / AP-2 adaptor complex / assembly chaperone
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / head development / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Retrograde neurotrophin signalling / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / Recycling pathway of L1 / postsynaptic neurotransmitter receptor internalization ...regulation of clathrin-dependent endocytosis / head development / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Retrograde neurotrophin signalling / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / Recycling pathway of L1 / postsynaptic neurotransmitter receptor internalization / AP-2 adaptor complex / cilium organization / membrane coat / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin-cargo adaptor activity / MHC class II antigen presentation / clathrin-dependent endocytosis / regulation of hematopoietic stem cell differentiation / synaptic vesicle endocytosis / vesicle-mediated transport / Neutrophil degranulation / clathrin-coated pit / phosphatidylinositol binding / secretory granule / protein serine/threonine kinase binding / intracellular protein transport / kinase binding / disordered domain specific binding / synaptic vesicle / cytoplasmic vesicle / cytoplasmic side of plasma membrane / postsynapse / protein domain specific binding / protein kinase binding / synapse / protein-containing complex binding / plasma membrane
Similarity search - Function
Coiled-coil domain containing protein 32 / Coiled-coil domain containing 32 / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain ...Coiled-coil domain containing protein 32 / Coiled-coil domain containing 32 / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / TBP domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
AP-2 complex subunit alpha-2 / Coiled-coil domain-containing protein 32
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSloan, D.E. / Matthews, A.E. / Tedamrongwanish, T. / Nicely, N.I. / Baker, R.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150960 United States
CitationJournal: Biorxiv / Year: 2025
Title: CCDC32 collaborates with the membrane to assemble the AP-2 clathrin adaptor complex.
Authors: Sloan, D.E. / Matthews, A. / Yanagisawa, H. / Tedamrongwanish, T. / Cannon, K. / Simmons, J. / Chappell, G. / Nicely, N.I. / Berlow, R. / Kikkawa, M. / Baker, R.W.
History
DepositionJul 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP-2 complex subunit alpha-2
B: AP-2 complex subunit alpha-2
P: Coiled-coil domain-containing protein 32
Q: Coiled-coil domain-containing protein 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6526
Polymers61,1754
Non-polymers4772
Water9,818545
1
A: AP-2 complex subunit alpha-2
P: Coiled-coil domain-containing protein 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8263
Polymers30,5882
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-14 kcal/mol
Surface area13150 Å2
MethodPISA
2
B: AP-2 complex subunit alpha-2
Q: Coiled-coil domain-containing protein 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8263
Polymers30,5882
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-14 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.664, 96.664, 195.231
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein AP-2 complex subunit alpha-2 / 100 kDa coated vesicle protein C / Adaptor protein complex AP-2 subunit alpha-2 / Adaptor-related ...100 kDa coated vesicle protein C / Adaptor protein complex AP-2 subunit alpha-2 / Adaptor-related protein complex 2 subunit alpha-2 / Alpha-adaptin C / Alpha2-adaptin / Clathrin assembly protein complex 2 alpha-C large chain / Plasma membrane adaptor HA2/AP2 adaptin alpha C subunit


Mass: 27509.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2a2, Adtab / Production host: Escherichia coli (E. coli) / References: UniProt: P17427
#2: Protein/peptide Coiled-coil domain-containing protein 32


Mass: 3078.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8BS39
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM SPG pH 8.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Feb 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→24.17 Å / Num. obs: 79167 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 20.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.042 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3930 / CC1/2: 0.863 / Rpim(I) all: 0.283 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→23.43 Å / SU ML: 0.2388 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.1506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2049 3981 5.03 %
Rwork0.1681 75186 -
obs0.17 79167 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.74 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 32 545 4809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784400
X-RAY DIFFRACTIONf_angle_d0.90285959
X-RAY DIFFRACTIONf_chiral_restr0.0533665
X-RAY DIFFRACTIONf_plane_restr0.0062793
X-RAY DIFFRACTIONf_dihedral_angle_d17.30711645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.2781400.26342517X-RAY DIFFRACTION97.61
2.13-2.150.28241390.23972774X-RAY DIFFRACTION98.41
2.15-2.180.29991380.23592650X-RAY DIFFRACTION99.15
2.18-2.210.29571370.22892661X-RAY DIFFRACTION99.86
2.21-2.240.23171480.22462710X-RAY DIFFRACTION100
2.24-2.280.30421420.21382673X-RAY DIFFRACTION100
2.28-2.310.30121460.21912728X-RAY DIFFRACTION99.93
2.31-2.350.24151480.20942671X-RAY DIFFRACTION99.96
2.35-2.390.25071340.20072662X-RAY DIFFRACTION100
2.39-2.430.28551420.19962689X-RAY DIFFRACTION99.96
2.43-2.480.27371500.19262748X-RAY DIFFRACTION100
2.48-2.530.211440.18922648X-RAY DIFFRACTION100
2.53-2.590.27241440.1832681X-RAY DIFFRACTION99.96
2.59-2.650.22921420.17552671X-RAY DIFFRACTION100
2.65-2.710.25271420.17792664X-RAY DIFFRACTION100
2.71-2.780.2211400.16632731X-RAY DIFFRACTION99.9
2.78-2.870.21781360.18782732X-RAY DIFFRACTION100
2.87-2.960.25651410.17752672X-RAY DIFFRACTION99.96
2.96-3.060.19421420.17442698X-RAY DIFFRACTION100
3.06-3.190.1981440.15242674X-RAY DIFFRACTION100
3.19-3.330.14841460.162684X-RAY DIFFRACTION100
3.33-3.510.1851460.14682706X-RAY DIFFRACTION100
3.51-3.730.16981400.13842716X-RAY DIFFRACTION100
3.73-4.010.18941480.13262664X-RAY DIFFRACTION100
4.01-4.410.12231340.12382714X-RAY DIFFRACTION100
4.41-5.050.15461400.12412708X-RAY DIFFRACTION100
5.05-6.330.15991320.15212658X-RAY DIFFRACTION100
6.34-23.430.17631560.15672682X-RAY DIFFRACTION98.95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.971933738975-0.00714580800705-0.08690622359195.14227764955-0.6320188976140.7634208832530.009228128616520.01838593791970.0177228986430.0673528706227-0.00349009792705-0.240024708901-0.08813421160090.0404743172689-0.001509874462640.1054284412260.0180577812595-0.009479253939580.180289479091-0.02063190463840.11822218390730.8706933629-5.4405932612221.1946756469
23.110804234790.235160856887-0.4384660188772.42849947816-0.5866806449171.992783312590.02314870604060.0327718654876-0.198663704438-0.02495646998450.01511358402110.1397943338150.00358826555784-0.11059434811-0.03415881089990.1113344635580.00770802114162-0.0138445125610.119700555617-0.0162576037930.13966668099417.9831605651-29.824585679127.0163480711
30.6901880360430.2528655937460.1275656468675.20127150046-0.7906659870690.856143666090.00122432470868-0.045871736944-0.00538691958201-0.05336764241160.00840484050468-0.2621010376180.07269575057360.0608009629683-0.007321409015510.0988352709598-0.01048696508240.01040340786760.184899057315-0.0259578175570.13177624402930.86010670485.42748351934-3.30918584769
43.0694344653-0.3214616145360.5916231735542.50248528585-0.603467262622.00320538838-0.000588990797694-0.02965283929960.2055236638810.03593011606050.02252607081610.157177949287-0.00394977613587-0.12521493543-0.01228908846840.110188684891-0.01008833700980.02438468448110.124887520032-0.0193331427620.14925887977118.21536068929.8079047208-9.11101089656
55.70124179969-3.312873203821.815617916397.10007173627-1.217327597912.767941134460.2491066666640.539929835588-0.156624318131-0.698360808546-0.0871668870897-0.134897029687-0.0082593016980.338457857174-0.200708349650.22626836339-0.01387845392630.08737264371540.163928614483-0.05026514187520.3038019772631.1030884118-39.405396471719.1324827026
69.41799399773-3.499442945931.785859258153.187469186840.4444422543082.98577969534-0.00934212847263-0.54366620832-0.5197718106640.6321146610470.08229624557540.8037991830360.440477798916-0.562190938317-0.08595489724340.3228007827130.04185659245070.04022895079570.2412530338070.02371518317570.44861894868925.8060411922-45.053106189932.156149944
70.00973952586245-0.03116035416240.0632869459760.290174489211-0.5383023743311.00336248529-0.130003993772-0.0630601554110.1627549380960.0664778048503-0.07639213371730.41804460942-0.07790920257420.1960972889910.1992603936781.26271651258-0.169973498552-0.122307014360.44509245242-0.04674272398360.7546723484917.6726602351-48.62602083125.5009622713
82.065985241021.892039302310.4876813047312.52795945827-1.053202959283.004539068790.186164144456-0.1513258873070.183616254854-0.06269035360970.03719831288510.305179019920.204811517435-0.228879928744-0.2028624202240.227363758081-0.04736275305750.04237446424020.1925047492350.01526517628310.37908100329710.8280586868-38.190888595833.1719240116
95.442397283712.68308243192-1.229179560146.7233818713-0.9171312148661.88357231520.41512313868-0.3287589256910.02927307710610.861061863787-0.0509548839292-0.357657631385-0.01065860997520.339257052123-0.3668256566070.2393119756390.00961285583938-0.109130284160.177358577284-0.06889871260170.31943778377831.109034467439.4278139279-1.23160404696
102.880859280562.46001416199-0.9522822335182.652193612940.3380356670862.718705232060.4530110211730.4042732659490.486567431923-0.321192412061-0.1135205167320.906824369171-0.782805863319-0.215898111874-0.3377299510250.330281308424-0.02675494077270.02213091178530.2314305658060.08140428891870.47107980759725.876035073445.1209305823-14.2744974325
110.523280811552-0.733700538872-0.3644282248661.057762075440.6315790563310.7574914633530.00487447939647-0.002588660029550.2734012147970.0238404411837-0.1464554883240.5733461148060.01863377945930.1460501363610.1315803835490.780988088635-0.0279547358931-0.04646625869110.406010665154-0.1683805676740.95598518345117.715936409248.6485520684-7.58642794025
121.73760210426-1.819421053810.03826236751631.92258729062-0.1709300854034.595178204590.1669029909140.1252742464650.287547391858-0.185087039375-0.0870687878242-0.0136545227901-0.484576622176-0.287552855454-0.05434900844380.2427659682550.03140594081220.008879779555410.2289477800070.07400589207620.35953159394110.658184033838.1527288011-15.4622767972
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 700 through 828 )AA700 - 8281 - 129
22chain 'A' and (resid 829 through 938 )AA829 - 938130 - 239
33chain 'B' and (resid 700 through 828 )BB700 - 8281 - 129
44chain 'B' and (resid 829 through 938 )BB829 - 938130 - 239
55chain 'P' and (resid 2 through 12 )PC2 - 121 - 11
66chain 'P' and (resid 13 through 17 )PC13 - 1712 - 16
77chain 'P' and (resid 18 through 22 )PC18 - 2217 - 21
88chain 'P' and (resid 23 through 29 )PC23 - 2922 - 28
99chain 'Q' and (resid 2 through 12 )QD2 - 121 - 11
1010chain 'Q' and (resid 13 through 17 )QD13 - 1712 - 16
1111chain 'Q' and (resid 18 through 22 )QD18 - 2217 - 21
1212chain 'Q' and (resid 23 through 29 )QD23 - 2922 - 28

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