6P5T

Surface-layer (S-layer) RsaA protein from Caulobacter crescentus bound to strontium and iodide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly.

Herrmann, J.Li, P.N.Jabbarpour, F.Chan, A.C.K.Rajkovic, I.Matsui, T.Shapiro, L.Smit, J.Weiss, T.M.Murphy, M.E.P.Wakatsuki, S.

(2020) Proc Natl Acad Sci U S A 117: 388-394

  • DOI: 10.1073/pnas.1909798116
  • Primary Citation of Related Structures:  
    6P5T

  • PubMed Abstract: 
  • Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown ...

    Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that the Caulobacter crescentus SLP readily crystallizes into sheets in vitro via a calcium-triggered multistep assembly pathway. This pathway involves 2 domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2-dimensional (2D) crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using a time course of electron cryo-microscopy (Cryo-EM) imaging reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the 2 domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.


    Organizational Affiliation

    Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S-layer protein
A, B, C, D, E, F
A, B, C, D, E, F
814Caulobacter vibrioidesMutation(s): 0 
Gene Names: rsaACC_1007
UniProt
Find proteins for P35828 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Explore P35828 
Go to UniProtKB:  P35828
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35828
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth A],
AC [auth B],
AD [auth C],
AF [auth D],
AG [auth E],
AA [auth A],
AC [auth B],
AD [auth C],
AF [auth D],
AG [auth E],
AI [auth F],
BA [auth A],
BD [auth C],
BF [auth D],
BG [auth E],
BI [auth F],
CA [auth A],
CD [auth C],
CF [auth D],
CG [auth E],
CI [auth F],
DA [auth A],
DB [auth B],
DD [auth C],
DF [auth D],
DG [auth E],
DI [auth F],
EA [auth A],
EB [auth B],
ED [auth C],
EF [auth D],
EG [auth E],
EI [auth F],
FA [auth A],
FB [auth B],
FD [auth C],
FF [auth D],
FG [auth E],
FI [auth F],
G [auth A],
GA [auth A],
GB [auth B],
GD [auth C],
GF [auth D],
GG [auth E],
GI [auth F],
H [auth A],
HA [auth A],
HB [auth B],
HD [auth C],
HG [auth E],
HI [auth F],
I [auth A],
IA [auth A],
IB [auth B],
ID [auth C],
IG [auth E],
II [auth F],
J [auth A],
JB [auth B],
JD [auth C],
JG [auth E],
JI [auth F],
K [auth A],
KB [auth B],
KD [auth C],
KE [auth D],
KG [auth E],
KI [auth F],
L [auth A],
LB [auth B],
LD [auth C],
LE [auth D],
LG [auth E],
LI [auth F],
M [auth A],
MB [auth B],
MD [auth C],
ME [auth D],
MG [auth E],
MI [auth F],
N [auth A],
NB [auth B],
ND [auth C],
NE [auth D],
NG [auth E],
NI [auth F],
O [auth A],
OB [auth B],
OD [auth C],
OE [auth D],
OG [auth E],
OI [auth F],
P [auth A],
PB [auth B],
PE [auth D],
PG [auth E],
PI [auth F],
Q [auth A],
QB [auth B],
QE [auth D],
QG [auth E],
QI [auth F],
R [auth A],
RB [auth B],
RE [auth D],
RG [auth E],
RI [auth F],
S [auth A],
SB [auth B],
SE [auth D],
SG [auth E],
SI [auth F],
T [auth A],
TB [auth B],
TE [auth D],
TG [auth E],
TH [auth F],
TI [auth F],
U [auth A],
UB [auth B],
UE [auth D],
UG [auth E],
UH [auth F],
UI [auth F],
V [auth A],
VB [auth B],
VC [auth C],
VE [auth D],
VG [auth E],
VH [auth F],
VI [auth F],
W [auth A],
WB [auth B],
WC [auth C],
WE [auth D],
WG [auth E],
WH [auth F],
WI [auth F],
X [auth A],
XB [auth B],
XC [auth C],
XE [auth D],
XG [auth E],
XH [auth F],
Y [auth A],
YB [auth B],
YC [auth C],
YE [auth D],
YH [auth F],
Z [auth A],
ZB [auth B],
ZC [auth C],
ZE [auth D],
ZH [auth F]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SR
Query on SR

Download Ideal Coordinates CCD File 
AB [auth A],
AE [auth C],
AH [auth E],
AJ [auth F],
BB [auth A],
AB [auth A],
AE [auth C],
AH [auth E],
AJ [auth F],
BB [auth A],
BC [auth B],
BE [auth C],
BH [auth E],
BJ [auth F],
CB [auth A],
CC [auth B],
CE [auth C],
CH [auth E],
CJ [auth F],
DC [auth B],
DE [auth C],
DH [auth E],
DJ [auth F],
EC [auth B],
EE [auth C],
EH [auth E],
EJ [auth F],
FC [auth B],
FE [auth C],
FH [auth E],
FJ [auth F],
GC [auth B],
GE [auth C],
GH [auth E],
GJ [auth F],
HC [auth B],
HE [auth C],
HF [auth D],
HH [auth E],
HJ [auth F],
IC [auth B],
IE [auth C],
IF [auth D],
IH [auth E],
IJ [auth F],
JA [auth A],
JC [auth B],
JE [auth C],
JF [auth D],
JH [auth E],
JJ [auth F],
KA [auth A],
KC [auth B],
KF [auth D],
KH [auth E],
KJ [auth F],
LA [auth A],
LC [auth B],
LF [auth D],
LH [auth E],
LJ [auth F],
MA [auth A],
MC [auth B],
MF [auth D],
MH [auth E],
MJ [auth F],
NA [auth A],
NC [auth B],
NF [auth D],
NH [auth E],
NJ [auth F],
OA [auth A],
OC [auth B],
OF [auth D],
OH [auth E],
OJ [auth F],
PA [auth A],
PC [auth B],
PD [auth C],
PF [auth D],
PH [auth E],
PJ [auth F],
QA [auth A],
QC [auth B],
QD [auth C],
QF [auth D],
QH [auth E],
QJ [auth F],
RA [auth A],
RC [auth B],
RD [auth C],
RF [auth D],
RH [auth E],
RJ [auth F],
SA [auth A],
SC [auth B],
SD [auth C],
SF [auth D],
SH [auth E],
SJ [auth F],
TA [auth A],
TC [auth B],
TD [auth C],
TF [auth D],
TJ [auth F],
UA [auth A],
UC [auth B],
UD [auth C],
UF [auth D],
VA [auth A],
VD [auth C],
VF [auth D],
WA [auth A],
WD [auth C],
WF [auth D],
XA [auth A],
XD [auth C],
XF [auth D],
XI [auth F],
YA [auth A],
YD [auth C],
YF [auth D],
YG [auth E],
YI [auth F],
ZA [auth A],
ZD [auth C],
ZF [auth D],
ZG [auth E],
ZI [auth F]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.729α = 90
b = 80.564β = 117.44
c = 221.833γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2015-04802

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references