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- PDB-9ext: Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain... -

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Basic information

Entry
Database: PDB / ID: 9ext
TitleCrystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to APL2/AP-1 Beta peptide (LLDL)
Components
  • AP-1 complex subunit beta-1
  • Clathrin heavy chain
KeywordsENDOCYTOSIS / Clathrin / APL2 / AP-1 Beta / Adaptor protein
Function / homology
Function and homology information


vesicle targeting, trans-Golgi to endosome / Lysosome Vesicle Biogenesis / VLDLR internalisation and degradation / Clathrin-mediated endocytosis / Recycling pathway of L1 / RHOV GTPase cycle / LDL clearance / Cargo recognition for clathrin-mediated endocytosis / RHOU GTPase cycle / clathrin vesicle coat ...vesicle targeting, trans-Golgi to endosome / Lysosome Vesicle Biogenesis / VLDLR internalisation and degradation / Clathrin-mediated endocytosis / Recycling pathway of L1 / RHOV GTPase cycle / LDL clearance / Cargo recognition for clathrin-mediated endocytosis / RHOU GTPase cycle / clathrin vesicle coat / clathrin coat of trans-Golgi network vesicle / AP-1 adaptor complex / clathrin light chain binding / Golgi to vacuole transport / clathrin complex / Golgi to endosome transport / clathrin coat of coated pit / clathrin coat assembly / actin cortical patch / cortical actin cytoskeleton organization / clathrin binding / vesicle-mediated transport / clathrin-coated pit / receptor-mediated endocytosis / intracellular protein transport / endocytosis / structural molecule activity / plasma membrane / cytosol
Similarity search - Function
Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat ...Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / AP-1/2/4 complex subunit beta / AP complex subunit beta / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin heavy chain / AP-1 complex subunit beta-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsDefelipe, L.A. / Bento, I. / Garcia Alai, M.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission664726European Union
CitationJournal: Nat Commun / Year: 2024
Title: Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast.
Authors: Defelipe, L.A. / Veith, K. / Burastero, O. / Kupriianova, T. / Bento, I. / Skruzny, M. / Kolbel, K. / Uetrecht, C. / Thuenauer, R. / Garcia-Alai, M.M.
History
DepositionApr 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clathrin heavy chain
B: Clathrin heavy chain
D: AP-1 complex subunit beta-1
E: AP-1 complex subunit beta-1
F: AP-1 complex subunit beta-1
G: AP-1 complex subunit beta-1
H: AP-1 complex subunit beta-1


Theoretical massNumber of molelcules
Total (without water)86,7037
Polymers86,7037
Non-polymers00
Water1086
1
A: Clathrin heavy chain
D: AP-1 complex subunit beta-1
F: AP-1 complex subunit beta-1
G: AP-1 complex subunit beta-1


Theoretical massNumber of molelcules
Total (without water)43,8274
Polymers43,8274
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Clathrin heavy chain
E: AP-1 complex subunit beta-1
H: AP-1 complex subunit beta-1


Theoretical massNumber of molelcules
Total (without water)42,8763
Polymers42,8763
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.780, 141.780, 168.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid -2 through 360)
d_2ens_1(chain "B" and resid -2 through 360)
d_1ens_2chain "D"
d_2ens_2chain "E"
d_3ens_2chain "F"
d_1ens_3chain "G"
d_2ens_3chain "H"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ALAALAARGARGAA-2 - 3602 - 364
d_2ens_1ALAALAARGARGBB-2 - 3602 - 364
d_1ens_2GLNGLNLEULEUDC2 - 72 - 7
d_2ens_2GLNGLNLEULEUED2 - 72 - 7
d_3ens_2GLNGLNLEULEUFE2 - 72 - 7
d_1ens_3ASPASPASPASPGF3 - 63 - 6
d_2ens_3ASPASPASPASPHG3 - 63 - 6

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.293958514224, -0.601142329535, -0.743112569909), (-0.605827918781, -0.484162161646, 0.631315716624), (-0.739297588756, 0.635778971713, -0.221865216712)87.8913122206, 96.510934086, 4.52844670128
2given(-0.139919162643, -0.65715975771, -0.740650849437), (-0.486203520953, -0.606022235574, 0.629557929187), (-0.862571019765, 0.44819426908, -0.234719264282)88.7144601803, 99.9380151791, 13.194896794
3given(0.812978570779, 0.568174592474, -0.127449895728), (0.380644002784, -0.35292081459, 0.85472629641), (0.44065404412, -0.743387201327, -0.503189310603)-18.8723534092, 69.5617784172, 41.2806934482
4given(-0.0737198983369, -0.718115306939, -0.692008513335), (-0.531488965409, -0.558852671433, 0.636555709487), (-0.843851205034, 0.414721710996, -0.340471799406)98.6294413639, 102.691052502, 19.9960392139

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Components

#1: Protein Clathrin heavy chain


Mass: 40976.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CHC1, YGL206C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22137
#2: Protein/peptide
AP-1 complex subunit beta-1 / Beta-1-adaptin / Clathrin assembly protein complex 1 beta-1 large chain / Clathrin assembly protein ...Beta-1-adaptin / Clathrin assembly protein complex 1 beta-1 large chain / Clathrin assembly protein large beta-1 chain


Mass: 950.045 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36000
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.89 Å3/Da / Density % sol: 74.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 4M Sodium Formate

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.75→141.78 Å / Num. obs: 45340 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 92.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.022 / Rrim(I) all: 0.083 / Χ2: 1.01 / Net I/σ(I): 30
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 2.879 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4359 / CC1/2: 0.589 / Rpim(I) all: 0.785 / Rrim(I) all: 2.992 / Χ2: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→100.25 Å / SU ML: 0.4049 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2585 2259 4.99 %
Rwork0.2289 43006 -
obs0.2304 45265 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.39 Å2
Refinement stepCycle: LAST / Resolution: 2.75→100.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5909 0 0 6 5915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556009
X-RAY DIFFRACTIONf_angle_d0.92048165
X-RAY DIFFRACTIONf_chiral_restr0.0574978
X-RAY DIFFRACTIONf_plane_restr0.00651052
X-RAY DIFFRACTIONf_dihedral_angle_d20.16832163
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.21461419901
ens_2d_2CDX-RAY DIFFRACTIONTorsion NCS1.54806318152
ens_2d_3CDX-RAY DIFFRACTIONTorsion NCS3.89381754656
ens_3d_2FGX-RAY DIFFRACTIONTorsion NCS2.03150594506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.810.40611300.35962636X-RAY DIFFRACTION100
2.81-2.880.34171340.33592646X-RAY DIFFRACTION100
2.88-2.950.32551430.32552657X-RAY DIFFRACTION100
2.95-3.030.33721360.33722636X-RAY DIFFRACTION100
3.03-3.120.38771400.38892655X-RAY DIFFRACTION100
3.12-3.220.36321460.32972632X-RAY DIFFRACTION100
3.22-3.330.34881570.2942653X-RAY DIFFRACTION100
3.33-3.460.29441290.26032658X-RAY DIFFRACTION100
3.46-3.620.26981320.24952690X-RAY DIFFRACTION100
3.62-3.810.26011410.25182667X-RAY DIFFRACTION99.96
3.81-4.050.26631580.24852668X-RAY DIFFRACTION100
4.05-4.370.21351540.18812675X-RAY DIFFRACTION100
4.37-4.80.23391300.17312710X-RAY DIFFRACTION100
4.8-5.50.20981290.19452743X-RAY DIFFRACTION100
5.5-6.930.28071360.22852775X-RAY DIFFRACTION100
6.93-100.250.22911640.20162905X-RAY DIFFRACTION99.9
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)
11.02658585393-0.14158379007-0.5639786435651.660170191541.384065730211.62327865975-0.139218510853-0.3180026436450.760335814340.03303528408320.25757049976-0.127675053994-0.43886019361-0.142110640796-1.7876171186E-61.205653738210.0951712229981-0.05951398102931.12796540685-0.2142763927841.2211026935618.677442279269.85300008024.0883236568
22.93805065610.1320723160011.943970701471.924363109780.1846283907011.333998592860.216813656704-0.3308719742340.63406776947-0.347949226725-0.1517347299810.307175751847-0.613238783449-0.7035637674630.0004179787047751.388995382630.204301016806-0.1029760204181.09982588249-0.1427228792571.401039424291.0682324960973.2847895719-3.41083420997
31.62817637504-0.3924818931931.24852476152.548467009250.472719721991.23502409861-0.0784632284683-0.2217369534380.758106463173-0.570388400281-0.003878721182980.715627046696-0.326549673313-0.580121539275-5.5523662804E-51.14320134680.108482662918-0.1963699833471.12167909663-0.2215006623031.24298217996-4.0399662709858.7730877208-3.67853442076
43.803619240660.1804812531950.7776593201195.078425518590.7115109159020.9401422432270.181929684677-0.313746040629-0.227382986521-0.0197930507748-0.1755946030430.554879096292-0.0694525710816-0.3225655393070.0002837193549690.7907156080260.0162327886279-0.06134441116980.947556742783-0.08696566923090.9103757026736.6020559640747.69484509862.45040399189
54.121190409990.7218545459751.110929704044.497437190430.9747330571461.744453760990.00777326255773-0.181255391405-0.1193653382980.1374955739590.07999659091230.1016032479960.05462139593740.153792288638.13712401976E-50.7525988146970.0154458518439-0.02492761064490.8684688692-0.08989685537540.73242310722321.042859800448.57870127364.52118418759
61.74245389338-0.07283344012290.175601685492.04495672846-0.7919224066550.3194410088620.3450283233240.1882571316520.634436672984-0.764241143278-0.24612317492-0.151324641528-0.847905880235-0.077991595392-0.0002952036875540.9356097131580.05726819803150.08306755014170.948026795831-0.1775699110660.96953012462520.307461989665.26201946932.53093422717
72.159654718121.38865211295-0.899591262591.728692164970.9508688409363.00805616796-0.903354228595-0.7477390004711.501770386980.5150940969740.294182807112-1.42261194218-0.6805194873930.0453357813452-0.01130427134910.844417186414-0.0339381021130.06316461954740.953186244477-0.2521477862390.95126003409248.452330230650.32242477965.285048534
82.58893285406-1.80184277108-0.7009316301792.60741826166-0.7225662879781.76718866684-0.3132585762660.0993536752321-0.4237331856680.376733486621-0.02014278703580.6767672821260.4771246126120.11688231532-0.02152786128821.07618840135-0.08223392468170.08547668811430.984652861874-0.08779031775691.1577695980436.885456338353.476261620433.4149403629
91.837765237710.7500940418791.078083245960.900397342185-0.09659643012721.11996059885-0.747330187037-0.944378017863-0.7749432801291.135657916270.6443464574560.3357739891010.349579311846-0.4265279497120.004307145222321.548050355590.2390966349840.1514574164741.266946191930.08046655526941.1222310856939.33493972654.589971418949.7372351426
102.903383409020.629041723817-1.938985911321.282372525370.7556697338072.81631116866-0.164919911233-1.406375341280.1312205181950.6015487712960.45617745428-0.7636249007790.2548407124690.889034611134-0.0002202841827241.185767222210.0717618565107-0.2097461941641.6176513086-0.3105753407981.0919857993753.78401543464.612182251448.7837887207
113.05883016948-0.171742193722-1.077610112963.918117543361.628273830143.330649149010.235353566079-0.1579044517670.701893515335-0.230385309970.214220818962-0.926413645765-0.3141344991820.5173092743580.0005817159007990.884292294738-0.1268905978880.1213660750570.979658763582-0.2645226534551.0028129337454.576015667870.599850444727.2324952807
123.529137084370.114505699357-2.004575610654.983410292040.2636409761934.503488610140.1517893184550.124745931516-0.227182153297-0.0494102893398-0.152194877946-0.128537868285-0.008081880794150.1356529940881.56568922303E-50.877855198634-0.0263007800513-0.03000193599290.906037090183-0.226068367820.83887569679346.279061733558.94482037922.5125379142
131.056803099640.413121907671-0.192381615881.114128522680.4920322016110.363893540167-0.171801331941-0.65920758388-0.128221473261-0.209352671087-0.0294170654122-0.03175837657230.753865236242-1.54452570861-0.001042597415770.834163916480.01919127540180.07095297590870.923571569714-0.1162345132540.81199983997839.48313797845.86317255483.44122963153
14-0.000623458739625-0.03480260866320.01562603984572.57689229858-1.068441831760.4467372469530.0714759060121-1.06841476404-1.333254350790.9286448908950.4436444757290.7290081279822.06715198352-0.3203278878560.02456171064871.08202173595-0.1642582781510.03729880179931.08705159556-0.09100750279131.582290474128.2826523122535.30542580083.82842102119
150.11671486577-0.416073806420.412827011512.52594343315-1.812403178271.54171780658-1.243543189831.046944940360.6642389980120.167721622957-0.811401460312-1.30209419138-0.9794214900730.1844154113290.02521445656171.31859510123-0.3231740417640.115930368591.2121559232-0.06582865508631.1199890433561.498662174476.918089059420.9747157239
160.266442467273-0.09226466446160.1531683543010.0318018740968-0.05321242817510.08671463862640.264635223856-0.8212526071721.777305182710.7366761075030.2716083637-0.568931523135-0.903651079265-0.240281831650.009830696824461.35823307018-0.01491506275510.02482320123561.28447353245-0.3075967812961.69671746937.5217443685263.521894342716.6955338635
170.00142361819816-0.00308478730187-0.001422540292270.0042446986107-0.00415776161669-5.74168752451E-50.0936907697811-0.1374711901410.784572807899-0.430534044710.3430135096870.5406745364-0.5549011563-0.9972460210410.006468194125571.550983379640.263635462563-0.3345773522421.40129263451-0.0534571147371.6145175753-7.358316377677.3028019127-4.65178644663
180.278436570257-0.549062643139-0.2338380711161.211759851610.2739839408820.434560539414-0.50041485458-0.296882957455-1.15808229445-0.0606803141516-0.4625387770360.5051860486470.19442731807-0.637234551119-0.03140530839442.01099147729-0.02893423081080.07700193154841.84193114704-0.3213427685771.4322640912846.867232997460.423325920759.8181375931
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 35 )AA-2 - 351 - 38
22chain 'A' and (resid 36 through 103 )AA36 - 10339 - 106
33chain 'A' and (resid 104 through 141 )AA104 - 141107 - 144
44chain 'A' and (resid 142 through 216 )AA142 - 216145 - 219
55chain 'A' and (resid 217 through 303 )AA217 - 303220 - 306
66chain 'A' and (resid 304 through 336 )AA304 - 336307 - 339
77chain 'A' and (resid 337 through 367 )AA337 - 367340 - 370
88chain 'B' and (resid -3 through 35 )BB-3 - 351 - 39
99chain 'B' and (resid 36 through 64 )BB36 - 6440 - 68
1010chain 'B' and (resid 65 through 141 )BB65 - 14169 - 145
1111chain 'B' and (resid 142 through 238 )BB142 - 238146 - 242
1212chain 'B' and (resid 239 through 336 )BB239 - 336243 - 340
1313chain 'B' and (resid 337 through 360 )BB337 - 360341 - 364
1414chain 'D' and (resid 2 through 7 )DD2 - 71 - 6
1515chain 'E' and (resid 2 through 7 )EE2 - 71 - 6
1616chain 'F' and (resid 2 through 7 )FF2 - 71 - 6
1717chain 'G' and (resid 3 through 6 )GG3 - 61 - 4
1818chain 'H' and (resid 3 through 6 )HH3 - 61 - 4

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