7RTH

Crystal structure of an anti-lysozyme nanobody in complex with an anti-nanobody Fab "NabFab"


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins.

Bloch, J.S.Mukherjee, S.Kowal, J.Filippova, E.V.Niederer, M.Pardon, E.Steyaert, J.Kossiakoff, A.A.Locher, K.P.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2115435118
  • Primary Citation of Related Structures:  
    7PHP, 7PHQ, 7PIJ, 7RTH

  • PubMed Abstract: 

    With conformation-specific nanobodies being used for a wide range of structural, biochemical, and cell biological applications, there is a demand for antigen-binding fragments (Fabs) that specifically and tightly bind these nanobodies without disturbing the nanobody-target protein interaction. Here, we describe the development of a synthetic Fab (termed NabFab) that binds the scaffold of an alpaca-derived nanobody with picomolar affinity. We demonstrate that upon complementary-determining region grafting onto this parent nanobody scaffold, nanobodies recognizing diverse target proteins and derived from llama or camel can cross-react with NabFab without loss of affinity. Using NabFab as a fiducial and size enhancer (50 kDa), we determined the high-resolution cryogenic electron microscopy (cryo-EM) structures of nanobody-bound VcNorM and ScaDMT, both small membrane proteins of ∼50 kDa. Using an additional anti-Fab nanobody further facilitated reliable initial three-dimensional structure determination from small cryo-EM test datasets. Given that NabFab is of synthetic origin, is humanized, and can be conveniently expressed in Escherichia coli in large amounts, it may be useful not only for structural biology but also for biomedical applications.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fragment Antigen-Binding Light Chain
A, C, E, G, I
A, C, E, G, I, K, M, O, Q
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fragment Antigen-Binding Heavy Chain
B, D, F, H, J
B, D, F, H, J, L, N, P, R
239Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody129Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
GC [auth N],
JB [auth H],
ZA [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

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AB [auth G]
AC [auth M]
BA [auth B]
BB [auth G]
BC [auth M]
AB [auth G],
AC [auth M],
BA [auth B],
BB [auth G],
BC [auth M],
CB [auth G],
CC [auth M],
CD [auth i],
DD [auth i],
ED [auth i],
FA [auth C],
GA [auth C],
GD [auth m],
HA [auth C],
HB [auth H],
HC [auth O],
HD [auth m],
IA [auth C],
IC [auth O],
ID [auth o],
JA [auth C],
JD [auth o],
KB [auth I],
KC [auth Q],
KD [auth o],
LB [auth I],
LC [auth R],
LD [auth q],
MB [auth I],
NA [auth D],
NB [auth I],
OA [auth D],
PC [auth a],
QB [auth J],
QC [auth a],
RA [auth E],
RB [auth J],
RC [auth c],
SA [auth E],
SC [auth c],
TA [auth E],
TB [auth K],
UA [auth E],
UB [auth K],
UC [auth e],
VC [auth e],
WC [auth e],
XB [auth L],
YC [auth g],
ZC [auth g]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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EA [auth B]
FB [auth G]
FD [auth k]
GB [auth G]
MA [auth C]
EA [auth B],
FB [auth G],
FD [auth k],
GB [auth G],
MA [auth C],
PB [auth I],
TC [auth c],
XA [auth E],
ZB [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

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AD [auth g]
BD [auth g]
CA [auth B]
DA [auth B]
DB [auth G]
AD [auth g],
BD [auth g],
CA [auth B],
DA [auth B],
DB [auth G],
DC [auth M],
EB [auth G],
EC [auth N],
FC [auth N],
IB [auth H],
JC [auth P],
KA [auth C],
LA [auth C],
MC [auth R],
MD [auth q],
NC [auth R],
ND [auth q],
OB [auth I],
OC [auth R],
PA [auth D],
QA [auth D],
SB [auth J],
VA [auth E],
VB [auth K],
WA [auth E],
WB [auth K],
XC [auth e],
YA [auth F],
YB [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.53α = 90
b = 130.28β = 107.99
c = 223.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description