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 6WL7 | pdb_00006wl7

Cryo-EM of Form 2 like peptide filament, 29-20-2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 6WL7

This is version 1.3 of the entry. See complete history. 

Literature

Structural analysis of cross alpha-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials.

Wang, F., Gnewou, O., Modlin, C., Beltran, L.C., Xu, C., Su, Z., Juneja, P., Grigoryan, G., Egelman, E.H., Conticello, V.P.

(2021) Nat Commun 12: 407-407

  • DOI: https://doi.org/10.1038/s41467-020-20689-w
  • Primary Citation Related Structures: 
    6WKX, 6WKY, 6WL0, 6WL1, 6WL7, 6WL8, 6WL9

  • PubMed Abstract: 

    The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.


  • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.

Macromolecule Content 

  • Total Structure Weight: 488.07 kDa 
  • Atom Count: 34,350 
  • Modeled Residue Count: 4,350 
  • Deposited Residue Count: 4,350 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
peptide 29-20-2
A,
AA [auth u],
AB [auth GA],
AC [auth N],
AD [auth xA],
AE [auth JB],
B [auth Z],
BA [auth v],
BB [auth HA],
BC [auth cA],
BD [auth yA],
BE [auth KB],
C [auth a],
CA [auth w],
CB [auth J],
CC [auth dA],
CD [auth zA],
CE [auth W],
D [auth b],
DA [auth x],
DB [auth IA],
DC [auth eA],
DD [auth 0A],
DE [auth LB],
E [auth c],
EA [auth F],
EB [auth JA],
EC [auth fA],
ED [auth S],
EE [auth MB],
F [auth d],
FA [auth y],
FB [auth KA],
FC [auth gA],
FD [auth 1A],
FE [auth NB],
G [auth B],
GA [auth z],
GB [auth LA],
GC [auth O],
GD [auth 2A],
GE [auth OB],
H [auth e],
HA [auth 0],
HB [auth MA],
HC [auth hA],
HD [auth 3A],
HE [auth PB],
I [auth f],
IA [auth 1],
IB [auth K],
IC [auth iA],
ID [auth 4A],
IE [auth X],
J [auth g],
JA [auth 2],
JB [auth NA],
JC [auth jA],
JD [auth 5A],
JE [auth QB],
K [auth h],
KA [auth G],
KB [auth OA],
KC [auth kA],
KD [auth T],
KE [auth RB],
L [auth i],
LA [auth 3],
LB [auth PA],
LC [auth lA],
LD [auth 6A],
LE [auth SB],
M [auth C],
MA [auth 4],
MB [auth QA],
MC [auth P],
MD [auth 7A],
ME [auth TB],
N [auth j],
NA [auth 5],
NB [auth RA],
NC [auth mA],
ND [auth 8A],
NE [auth UB],
O [auth k],
OA [auth 6],
OB [auth L],
OC [auth nA],
OD [auth 9A],
OE [auth Y],
P [auth l],
PA [auth 7],
PB [auth SA],
PC [auth oA],
PD [auth AB],
PE [auth VB],
Q [auth m],
QA [auth H],
QB [auth TA],
QC [auth pA],
QD [auth U],
QE [auth WB],
R [auth n],
RA [auth 8],
RB [auth UA],
RC [auth qA],
RD [auth BB],
RE [auth XB],
S [auth D],
SA [auth 9],
SB [auth VA],
SC [auth Q],
SD [auth CB],
SE [auth YB],
T [auth o],
TA [auth AA],
TB [auth WA],
TC [auth rA],
TD [auth DB],
TE [auth ZB],
U [auth p],
UA [auth BA],
UB [auth M],
UC [auth sA],
UD [auth EB],
V [auth q],
VA [auth CA],
VB [auth XA],
VC [auth tA],
VD [auth FB],
W [auth r],
WA [auth I],
WB [auth YA],
WC [auth uA],
WD [auth V],
X [auth s],
XA [auth DA],
XB [auth ZA],
XC [auth vA],
XD [auth GB],
Y [auth E],
YA [auth EA],
YB [auth aA],
YC [auth R],
YD [auth HB],
Z [auth t],
ZA [auth FA],
ZB [auth bA],
ZC [auth wA],
ZD [auth IB]
29synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF-DMR-1533958

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2025-05-14
    Changes: Data collection, Structure summary