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- PDB-8r8b: Wnt binding to COPalpha and COPBeta2 directs secretion on extrace... -

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Basic information

Entry
Database: PDB / ID: 8r8b
TitleWnt binding to COPalpha and COPBeta2 directs secretion on extracellular vesicles
Components
  • Coatomer subunit beta'
  • Small ribosomal subunit protein mS37
KeywordsTRANSPORT PROTEIN / Wnt signalling / Coatomer complex / Wnt7a / Regenerative myogenesis / COPI vesicles / COPalpha / COPBeta2 / Extracellular vesicles / Exosomes / Signal peptide.
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitochondrial small ribosomal subunit / mitochondrial translation / endoplasmic reticulum to Golgi vesicle-mediated transport ...COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitochondrial small ribosomal subunit / mitochondrial translation / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / intracellular protein transport / mitochondrial inner membrane / structural constituent of ribosome / Golgi membrane / structural molecule activity
Similarity search - Function
Ribosomal protein MRP10, mitochondrial / Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. ...Ribosomal protein MRP10, mitochondrial / Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Small ribosomal subunit protein mS37 / Coatomer subunit beta'
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.808 Å
AuthorsGurriaran-Rodriguez, U. / Datzkiw, D. / Radusky, L.G. / Fisher, F. / Xiao, F. / Ming, H. / De Repentigny, Y. / Kothary, R. / Serrano, L. / Rojas, A.L. ...Gurriaran-Rodriguez, U. / Datzkiw, D. / Radusky, L.G. / Fisher, F. / Xiao, F. / Ming, H. / De Repentigny, Y. / Kothary, R. / Serrano, L. / Rojas, A.L. / Hierro, A. / Rudnicki, M.A.
Funding support Spain, Canada, 3items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BFU2017-88766-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119132GB-I00 Spain
Canadian Institutes of Health Research (CIHR)FDN-148387 Canada
CitationJournal: Sci Adv / Year: 2024
Title: Identification of the Wnt signal peptide that directs secretion on extracellular vesicles.
Authors: Gurriaran-Rodriguez, U. / Datzkiw, D. / Radusky, L.G. / Esper, M. / Javandoost, E. / Xiao, F. / Ming, H. / Fisher, S. / Marina, A. / De Repentigny, Y. / Kothary, R. / Azkargorta, M. / ...Authors: Gurriaran-Rodriguez, U. / Datzkiw, D. / Radusky, L.G. / Esper, M. / Javandoost, E. / Xiao, F. / Ming, H. / Fisher, S. / Marina, A. / De Repentigny, Y. / Kothary, R. / Azkargorta, M. / Elortza, F. / Rojas, A.L. / Serrano, L. / Hierro, A. / Rudnicki, M.A.
History
DepositionNov 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Coatomer subunit beta'
BBB: Coatomer subunit beta'
CCC: Coatomer subunit beta'
DDD: Coatomer subunit beta'
EEE: Coatomer subunit beta'
FFF: Coatomer subunit beta'
GGG: Coatomer subunit beta'
HHH: Coatomer subunit beta'
III: Coatomer subunit beta'
JJJ: Coatomer subunit beta'
KKK: Coatomer subunit beta'
LLL: Coatomer subunit beta'
MMM: Coatomer subunit beta'
NNN: Coatomer subunit beta'
OOO: Coatomer subunit beta'
PPP: Coatomer subunit beta'
QQQ: Coatomer subunit beta'
RRR: Coatomer subunit beta'
SSS: Coatomer subunit beta'
TTT: Coatomer subunit beta'
UUU: Coatomer subunit beta'
VVV: Coatomer subunit beta'
WWW: Coatomer subunit beta'
XXX: Coatomer subunit beta'
aaa: Small ribosomal subunit protein mS37
bbb: Small ribosomal subunit protein mS37
ccc: Small ribosomal subunit protein mS37
ddd: Small ribosomal subunit protein mS37
eee: Small ribosomal subunit protein mS37
fff: Small ribosomal subunit protein mS37
ggg: Small ribosomal subunit protein mS37
hhh: Small ribosomal subunit protein mS37
iii: Small ribosomal subunit protein mS37
jjj: Small ribosomal subunit protein mS37
kkk: Small ribosomal subunit protein mS37
lll: Small ribosomal subunit protein mS37
mmm: Small ribosomal subunit protein mS37
nnn: Small ribosomal subunit protein mS37
ooo: Small ribosomal subunit protein mS37
ppp: Small ribosomal subunit protein mS37
qqq: Small ribosomal subunit protein mS37
rrr: Small ribosomal subunit protein mS37
sss: Small ribosomal subunit protein mS37
ttt: Small ribosomal subunit protein mS37
uuu: Small ribosomal subunit protein mS37
vvv: Small ribosomal subunit protein mS37
www: Small ribosomal subunit protein mS37
xxx: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)874,181311
Polymers849,14348
Non-polymers25,038263
Water60,3143348
1
AAA: Coatomer subunit beta'
aaa: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,09820
Polymers35,3812
Non-polymers1,71718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Coatomer subunit beta'
bbb: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33012
Polymers35,3812
Non-polymers94910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Coatomer subunit beta'
ccc: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,52214
Polymers35,3812
Non-polymers1,14112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Coatomer subunit beta'
ddd: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,52614
Polymers35,3812
Non-polymers1,14512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
EEE: Coatomer subunit beta'
eee: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,23411
Polymers35,3812
Non-polymers8539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
FFF: Coatomer subunit beta'
fff: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33012
Polymers35,3812
Non-polymers94910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
GGG: Coatomer subunit beta'
ggg: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9498
Polymers35,3812
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
HHH: Coatomer subunit beta'
hhh: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,71016
Polymers35,3812
Non-polymers1,32914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
III: Coatomer subunit beta'
iii: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33412
Polymers35,3812
Non-polymers95310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
JJJ: Coatomer subunit beta'
jjj: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,32612
Polymers35,3812
Non-polymers94510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
KKK: Coatomer subunit beta'
kkk: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,62215
Polymers35,3812
Non-polymers1,24113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
LLL: Coatomer subunit beta'
lll: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,53014
Polymers35,3812
Non-polymers1,14912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
MMM: Coatomer subunit beta'
mmm: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,42213
Polymers35,3812
Non-polymers1,04111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
NNN: Coatomer subunit beta'
nnn: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,62215
Polymers35,3812
Non-polymers1,24113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
OOO: Coatomer subunit beta'
ooo: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33812
Polymers35,3812
Non-polymers95710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
PPP: Coatomer subunit beta'
ppp: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33412
Polymers35,3812
Non-polymers95310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
QQQ: Coatomer subunit beta'
qqq: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33412
Polymers35,3812
Non-polymers95310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
RRR: Coatomer subunit beta'
rrr: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33812
Polymers35,3812
Non-polymers95710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
SSS: Coatomer subunit beta'
sss: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,71416
Polymers35,3812
Non-polymers1,33314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
20
TTT: Coatomer subunit beta'
ttt: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,23811
Polymers35,3812
Non-polymers8579
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
21
UUU: Coatomer subunit beta'
uuu: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,81017
Polymers35,3812
Non-polymers1,42915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
22
VVV: Coatomer subunit beta'
vvv: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,14510
Polymers35,3812
Non-polymers7658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
23
WWW: Coatomer subunit beta'
www: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9498
Polymers35,3812
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
24
XXX: Coatomer subunit beta'
xxx: Small ribosomal subunit protein mS37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,43013
Polymers35,3812
Non-polymers1,04911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.457, 160.656, 160.619
Angle α, β, γ (deg.)107.268, 107.157, 107.241
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
Coatomer subunit beta'


Mass: 34651.953 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC27 / Production host: Escherichia coli (E. coli) / References: UniProt: P41811
#2: Protein/peptide ...
Small ribosomal subunit protein mS37 / 37S ribosomal protein MRP10 / mitochondrial / YmS-T / Wnt7a


Mass: 728.985 Da / Num. of mol.: 24 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O75012
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 206 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.04 Å3/Da / Density % sol: 69.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 0.1M Hepes 7.0 2.0M AmSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979335 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2021
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979335 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.2633
pseudo-merohedral22-H, -L, -K20.0987
pseudo-merohedral33-L, -K, -H30.1089
pseudo-merohedral44K, L, H40.1906
pseudo-merohedral55L, H, K50.1977
pseudo-merohedral66-K, -H, -L60.1408
ReflectionResolution: 1.808→139.2 Å / Num. obs: 1088963 / % possible obs: 95.5 % / Redundancy: 3.5 % / CC1/2: 0.99 / Net I/σ(I): 8.53
Reflection shellResolution: 1.81→1.92 Å / Num. unique obs: 178778 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YNN

2ynn


Resolution: 1.808→49.377 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.438 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.021
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1744 44507 5.062 %
Rwork0.1594 834790 -
all0.16 --
obs-879297 72.385 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.112 Å2-7.736 Å2-11.265 Å2
2---2.889 Å28.738 Å2
3---3.001 Å2
Refinement stepCycle: LAST / Resolution: 1.808→49.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59524 0 1372 3348 64244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01362402
X-RAY DIFFRACTIONr_bond_other_d0.0010.01755954
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.64485015
X-RAY DIFFRACTIONr_angle_other_deg1.0411.577129999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.12157382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72822.4393079
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2811510115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8415312
X-RAY DIFFRACTIONr_chiral_restr0.0420.28087
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0267872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0213316
X-RAY DIFFRACTIONr_nbd_refined0.1710.210344
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.259233
X-RAY DIFFRACTIONr_nbtor_refined0.1570.228055
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.226824
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.23515
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.295
X-RAY DIFFRACTIONr_nbd_other0.1590.2317
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.283
X-RAY DIFFRACTIONr_mcbond_it0.7293.16129561
X-RAY DIFFRACTIONr_mcbond_other0.7293.16129560
X-RAY DIFFRACTIONr_mcangle_it1.2564.74136878
X-RAY DIFFRACTIONr_mcangle_other1.2564.74136879
X-RAY DIFFRACTIONr_scbond_it0.4783.24832841
X-RAY DIFFRACTIONr_scbond_other0.4783.24832842
X-RAY DIFFRACTIONr_scangle_it0.7884.8648119
X-RAY DIFFRACTIONr_scangle_other0.7884.8648120
X-RAY DIFFRACTIONr_lrange_it2.82135.57466958
X-RAY DIFFRACTIONr_lrange_other2.66935.45666512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.808-1.8550.2323000.2256018X-RAY DIFFRACTION7.0266
1.855-1.9060.22914190.21626006X-RAY DIFFRACTION31.2821
1.906-1.9610.22920710.20637726X-RAY DIFFRACTION46.6542
1.961-2.0210.20124810.19343405X-RAY DIFFRACTION55.5359
2.021-2.0880.21626910.19249971X-RAY DIFFRACTION65.6609
2.088-2.1610.21828810.18753222X-RAY DIFFRACTION72.3854
2.161-2.2420.20328520.17955198X-RAY DIFFRACTION77.4413
2.242-2.3340.2130360.17556061X-RAY DIFFRACTION82.1499
2.334-2.4380.20429070.18256662X-RAY DIFFRACTION86.1185
2.438-2.5570.21928240.256197X-RAY DIFFRACTION89.6295
2.557-2.6950.22529240.19756612X-RAY DIFFRACTION94.6895
2.695-2.8580.20128800.17754440X-RAY DIFFRACTION96.6725
2.858-3.0550.18424700.16751380X-RAY DIFFRACTION96.67
3.055-3.30.16926900.15947756X-RAY DIFFRACTION96.9705
3.3-3.6150.1625160.14943857X-RAY DIFFRACTION97.214
3.615-4.0410.13921800.12940158X-RAY DIFFRACTION97.7219
4.041-4.6660.12418910.11134899X-RAY DIFFRACTION96.798
4.666-5.7130.13715920.13629640X-RAY DIFFRACTION96.9216
5.713-8.0720.1712330.16322874X-RAY DIFFRACTION97.0999
8.072-49.3770.1666690.15712708X-RAY DIFFRACTION98.1078

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