4M63: Filament-Like Actin Trimer

Crystal Structure of a Filament-Like Actin Trimer Bound to the Bacterial Effector VopL. Determined by X-ray diffraction at 2.75 Å resolution. Released 23 Oct 2013.

Method
X-ray diffraction
Resolution
2.75 Å
Organisms
Vibrio parahaemolyticus, Drosophila melanogaster
Chains
5
Atoms
11,960
Mol. weight
180.7 kDa
Ligands
CA, ATP
Released
23 Oct 2013

Explore 4M63 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4M63 contains 99 α-helices and 62 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 3 β-strands

ElementResiduesLengthSheet
α-helix253-2564
α-helix257-2593
α-helix262-27918
α-helix284-2918
α-helix299-3013
α-helix306-31510
α-helix319-3213
α-helix324-3252
β-strand327-32821
α-helix341-35010
β-strand355-35952
β-strand365-36952
α-helix370-38415
α-helix387-3959
α-helix398-40710
α-helix410-4123
α-helix415-4195
α-helix421-43313
α-helix434-4363
α-helix441-45515
α-helix462-47211
Chain B: 16 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix253-2564
α-helix262-27918
α-helix284-2907
α-helix297-3004
α-helix306-31510
α-helix319-3213
α-helix323-3253
β-strand327-32823
α-helix340-35011
β-strand355-35954
β-strand365-36954
α-helix370-38213
α-helix388-3936
α-helix398-40811
α-helix410-4123
α-helix416-4194
α-helix421-43313
α-helix441-45515
α-helix462-47211
Chain C: 19 helices, 21 β-strands
ElementResiduesLengthSheet
β-strand8-1255
β-strand17-2155
β-strand2216
β-strand2416
β-strand29-3135
β-strand35-3847
β-strand53-5427
α-helix56-605
β-strand65-6847
β-strand71-7228
β-strand75-7628
α-helix79-8810
α-helix89-946
α-helix98-1003
β-strand103-10755
α-helix113-12513
β-strand131-13665
α-helix137-1448
β-strand149-15579
β-strand160-16679
β-strand169-17029
β-strand176-17839
α-helix182-19413
α-helix203-21614
α-helix223-23210
β-strand240-241210
β-strand247-248210
α-helix253-26210
α-helix264-2663
α-helix274-28310
α-helix290-2945
β-strand297-30049
α-helix302-3054
α-helix309-31911
β-strand329-33029
α-helix338-3469
β-strand357-35825
α-helix359-3657
α-helix367-3693
α-helix370-3734
Chain D: 25 helices, 19 β-strands
ElementResiduesLengthSheet
α-helix6-72
β-strand8-12511
β-strand16-21611
β-strand29-32411
β-strand35-37312
β-strand53-54212
α-helix56-605
β-strand66-68312
β-strand71-72213
β-strand75-76213
α-helix79-8810
α-helix89-946
α-helix98-1003
β-strand103-107511
α-helix113-12513
β-strand131-136611
α-helix137-1448
β-strand150-155614
β-strand160-166714
β-strand169-170214
β-strand176-178314
α-helix182-19211
α-helix193-1953
α-helix203-21614
α-helix223-23210
β-strand238-24141
β-strand247-25041
α-helix253-2564
α-helix258-2614
α-helix264-2674
α-helix272-2732
α-helix274-2829
α-helix290-2945
β-strand297-300414
α-helix302-3043
α-helix310-3189
α-helix326-3272
β-strand329-330214
α-helix338-34811
α-helix350-3523
β-strand357-358211
α-helix359-3657
α-helix367-3693
α-helix370-3734
Chain E: 21 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand8-11415
β-strand16-21615
β-strand22116
β-strand24116
β-strand29-32415
α-helix56-605
α-helix72-743
α-helix79-8810
α-helix89-946
β-strand103-107515
α-helix113-12513
β-strand131-136615
α-helix137-1448
β-strand150-155617
β-strand160-166717
β-strand169-170217
α-helix172-1743
β-strand176-178317
α-helix182-19211
α-helix206-21611
α-helix223-2308
β-strand238-24143
β-strand247-25043
α-helix253-2564
α-helix258-2614
α-helix264-2674
α-helix274-28310
α-helix287-2948
β-strand297-300417
α-helix302-3043
α-helix309-32012
β-strand329-330217
α-helix338-3469
β-strand357-358215
α-helix359-3657
α-helix367-3693
α-helix370-3734

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
T3SS2 effector VopL nucleation of actin polymerizationA, Bprotein241Vibrio parahaemolyticusQ87GE5 (AlphaFold model)
Actin-5CC, D, Eprotein377Drosophila melanogasterP10987 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>4M63_1 T3SS2 effector VopL nucleation of actin polymerization (chains A, B)
GHMRLLSEDLFKQSPKLSEQELDELANNLADYLFQAADIDWHQVISEKTRGLTTEEMAKS
EHRYVQAFCREILKYPDCYKSADVASPESPKSGGGSVIDVALKRLQTGRERLFTTTDEKG
NRELKKGDAILESAINAARMAISTEEKNTILSNNVKSATFDVFCELPCMDGFAEQNGKTA
FYALRAGFYSAFKNTDTAKQDITKFMKDNLQAGFSGYSYQGLTNRVAQLEAQLAALSAKL
S
Sequence of entity 2 (C, D, E), FASTA
>4M63_2 Actin-5C (chains C, D, E)
GMCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREK
MTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRL
DLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEK
SYELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCAAAIRKDLYANTV
LSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIS
KQEYDESGPSIVHRKCF

Ligands and cofactors

IDNameFormulaCopies
CACalcium ionCa3
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P33

Primary citation

The Bacterial Effector VopL Organizes Actin into Filament-like Structures. Zahm, J.A., Padrick, S.B., Chen, Z. et al. Cell (2013) 155:423-434. DOI 10.1016/j.cell.2013.09.019 · PubMed

Other PDB entries of the same protein (UniProt Q87GE5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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