8R8B | pdb_00008r8b

Wnt binding to COPalpha and COPBeta2 directs secretion on extracellular vesicles


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.174 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.195 (DCC) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of the Wnt signal peptide that directs secretion on extracellular vesicles.

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.

(2024) Sci Adv 10: eado5914-eado5914

  • DOI: https://doi.org/10.1126/sciadv.ado5914
  • Primary Citation of Related Structures:  
    8R8B

  • PubMed Abstract: 

    Wnt proteins are hydrophobic glycoproteins that are nevertheless capable of long-range signaling. We found that Wnt7a is secreted long distance on the surface of extracellular vesicles (EVs) following muscle injury. We defined a signal peptide region in Wnts required for secretion on EVs, termed exosome-binding peptide (EBP). Addition of EBP to an unrelated protein directed secretion on EVs. Palmitoylation and the signal peptide were not required for Wnt7a-EV secretion. Coatomer was identified as the EV-binding protein for the EBP. Analysis of cocrystal structures, binding thermodynamics, and mutagenesis found that a dilysine motif mediates EBP binding to coatomer with a conserved function across the Wnt family. We showed that EBP is required for Wnt7a bioactivity when expressed in vivo during regeneration. Overall, our study has elucidated the structural basis and singularity of Wnt secretion on EVs, alternatively to canonical secretion, opening avenues for innovative therapeutic targeting strategies and systemic protein delivery.


  • Organizational Affiliation
    • Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, Ontario, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coatomer subunit beta'304Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEC27
UniProt
Find proteins for P41811 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41811 
Go to UniProtKB:  P41811
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41811
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein mS376Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for O75012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O75012 
Go to UniProtKB:  O75012
Entity Groups  
UniProt GroupO75012
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth AAA]
AC [auth CCC]
AE [auth HHH]
AF [auth KKK]
AG [auth MMM]
AB [auth AAA],
AC [auth CCC],
AE [auth HHH],
AF [auth KKK],
AG [auth MMM],
AH [auth OOO],
AI [auth RRR],
AJ [auth TTT],
BB [auth AAA],
BC [auth CCC],
BF [auth KKK],
BG [auth MMM],
BH [auth OOO],
BI [auth RRR],
BJ [auth TTT],
BK [auth WWW],
CB [auth AAA],
CC [auth CCC],
CF [auth KKK],
CG [auth MMM],
CH [auth OOO],
CI [auth RRR],
CJ [auth TTT],
CK [auth WWW],
DB [auth AAA],
DC [auth CCC],
DD [auth FFF],
DF [auth KKK],
DG [auth MMM],
DI [auth RRR],
DK [auth WWW],
EB [auth AAA],
EC [auth CCC],
ED [auth FFF],
EF [auth KKK],
EH [auth PPP],
EI [auth RRR],
EK [auth WWW],
FB [auth AAA],
FD [auth FFF],
FE [auth III],
FF [auth KKK],
FH [auth PPP],
FI [auth RRR],
FJ [auth UUU],
GB [auth AAA],
GD [auth FFF],
GE [auth III],
GF [auth KKK],
GH [auth PPP],
GI [auth RRR],
GJ [auth UUU],
HB [auth AAA],
HD [auth FFF],
HE [auth III],
HF [auth KKK],
HH [auth PPP],
HJ [auth UUU],
HK [auth XXX],
IB [auth AAA],
IC [auth DDD],
ID [auth FFF],
IE [auth III],
IF [auth KKK],
IG [auth NNN],
IH [auth PPP],
II [auth SSS],
IJ [auth UUU],
IK [auth XXX],
JB [auth AAA],
JC [auth DDD],
JD [auth FFF],
JE [auth III],
JF [auth KKK],
JG [auth NNN],
JH [auth PPP],
JI [auth SSS],
JJ [auth UUU],
JK [auth XXX],
KC [auth DDD],
KE [auth III],
KG [auth NNN],
KH [auth PPP],
KI [auth SSS],
KJ [auth UUU],
KK [auth XXX],
LC [auth DDD],
LE [auth III],
LG [auth NNN],
LH [auth PPP],
LI [auth SSS],
LJ [auth UUU],
LK [auth XXX],
MC [auth DDD],
ME [auth III],
MF [auth LLL],
MG [auth NNN],
MI [auth SSS],
MJ [auth UUU],
MK [auth XXX],
NB [auth BBB],
NC [auth DDD],
ND [auth GGG],
NF [auth LLL],
NG [auth NNN],
NI [auth SSS],
NJ [auth UUU],
NK [auth XXX],
OB [auth BBB],
OC [auth DDD],
OD [auth GGG],
OF [auth LLL],
OG [auth NNN],
OH [auth QQQ],
OI [auth SSS],
OJ [auth UUU],
OK [auth XXX],
PB [auth BBB],
PC [auth DDD],
PE [auth JJJ],
PF [auth LLL],
PG [auth NNN],
PH [auth QQQ],
PI [auth SSS],
PJ [auth UUU],
PK [auth XXX],
QB [auth BBB],
QC [auth DDD],
QE [auth JJJ],
QF [auth LLL],
QG [auth NNN],
QH [auth QQQ],
QI [auth SSS],
QJ [auth UUU],
RB [auth BBB],
RC [auth DDD],
RD [auth HHH],
RE [auth JJJ],
RF [auth LLL],
RG [auth NNN],
RH [auth QQQ],
RI [auth SSS],
SB [auth BBB],
SD [auth HHH],
SE [auth JJJ],
SF [auth LLL],
SH [auth QQQ],
SI [auth SSS],
SK [auth aaa],
TB [auth BBB],
TD [auth HHH],
TE [auth JJJ],
TF [auth LLL],
TH [auth QQQ],
TK [auth ccc],
UC [auth EEE],
UD [auth HHH],
UE [auth JJJ],
UF [auth LLL],
UG [auth OOO],
UH [auth QQQ],
UJ [auth VVV],
UK [auth ggg],
VC [auth EEE],
VD [auth HHH],
VF [auth LLL],
VG [auth OOO],
VH [auth QQQ],
VJ [auth VVV],
VK [auth ggg],
WA [auth AAA],
WC [auth EEE],
WD [auth HHH],
WG [auth OOO],
WI [auth TTT],
WJ [auth VVV],
WK [auth lll],
XA [auth AAA],
XB [auth CCC],
XC [auth EEE],
XD [auth HHH],
XF [auth MMM],
XG [auth OOO],
XI [auth TTT],
XJ [auth VVV],
XK [auth nnn],
YA [auth AAA],
YB [auth CCC],
YC [auth EEE],
YD [auth HHH],
YF [auth MMM],
YG [auth OOO],
YH [auth RRR],
YI [auth TTT],
YJ [auth VVV],
YK [auth vvv],
ZA [auth AAA],
ZB [auth CCC],
ZC [auth EEE],
ZD [auth HHH],
ZE [auth KKK],
ZF [auth MMM],
ZG [auth OOO],
ZH [auth RRR],
ZI [auth TTT],
ZJ [auth VVV]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AD [auth EEE]
AK [auth VVV]
BD [auth EEE]
BE [auth HHH]
CD [auth EEE]
AD [auth EEE],
AK [auth VVV],
BD [auth EEE],
BE [auth HHH],
CD [auth EEE],
CE [auth HHH],
DE [auth HHH],
DH [auth OOO],
DJ [auth TTT],
EE [auth HHH],
EG [auth MMM],
EJ [auth TTT],
FC [auth CCC],
FG [auth MMM],
FK [auth WWW],
GC [auth CCC],
GG [auth MMM],
GK [auth WWW],
HC [auth CCC],
HG [auth MMM],
HI [auth RRR],
KB [auth AAA],
KD [auth FFF],
KF [auth KKK],
LB [auth AAA],
LD [auth FFF],
LF [auth KKK],
MB [auth AAA],
MD [auth FFF],
MH [auth PPP],
NE [auth III],
NH [auth PPP],
OE [auth III],
PD [auth GGG],
QD [auth GGG],
QK [auth XXX],
RJ [auth UUU],
RK [auth XXX],
SC [auth DDD],
SG [auth NNN],
SJ [auth UUU],
TC [auth DDD],
TG [auth NNN],
TI [auth SSS],
TJ [auth UUU],
UB [auth BBB],
UI [auth SSS],
VB [auth BBB],
VE [auth JJJ],
VI [auth SSS],
WB [auth BBB],
WE [auth JJJ],
WF [auth LLL],
WH [auth QQQ],
XE [auth JJJ],
XH [auth QQQ],
YE [auth JJJ]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.174 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.195 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.457α = 107.268
b = 160.656β = 107.157
c = 160.619γ = 107.241
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)SpainBFU2017-88766-R
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-119132GB-I00
Canadian Institutes of Health Research (CIHR)CanadaFDN-148387

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references