Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 118, Issue 47, Year 2021
Publish date	Nov 23, 2021
Authors	Joël S Bloch / Somnath Mukherjee / Julia Kowal / Ekaterina V Filippova / Martina Niederer / Els Pardon / Jan Steyaert / Anthony A Kossiakoff / Kaspar P Locher /
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 ...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 in large amounts, it may be useful not only for structural biology but also for biomedical applications.
External links	Proc Natl Acad Sci U S A / PubMed:34782475 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.19 - 8.45 Å
Structure data	13424 7php EMDB-13424, PDB-7php: Structure of Multidrug and Toxin Compound Extrusion (MATE) transporter NorM by NabFab-fiducial assisted cryo-EM Method: EM (single particle) / Resolution: 3.47 Å EMDB-13425: Map of complex of Vibrio cholerae MATE transporter NorM, chimeric nanobody NorM-Nb17_4, NabFab, and anti-Fab nanobody with fulcrum in center of micelle Method: EM (single particle) / Resolution: 3.68 Å 13426 7phq EMDB-13426, PDB-7phq: Structure of homo-dimeric Staphylococcus capitis divalent metal ion transporter (DMT) by NabFab-fiducial assisted cryo-EM Method: EM (single particle) / Resolution: 8.45 Å 13438 7pij EMDB-13438, PDB-7pij: Structure of Staphylococcus capitis divalent metal ion transporter (DMT) by NabFab-fiducial assisted cryo-EM Method: EM (single particle) / Resolution: 3.78 Å PDB-7rth: Crystal structure of an anti-lysozyme nanobody in complex with an anti-nanobody Fab "NabFab" Method: X-RAY DIFFRACTION / Resolution: 3.19 Å
Chemicals	ChemComp-HOH: WATER / Water ChemComp-PO4: PHOSPHATE ION / Phosphate ChemComp-CL: Unknown entry / Chloride ChemComp-GOL: GLYCEROL / Glycerol ChemComp-PEG: DI(HYDROXYETHYL)ETHER / Diethylene glycol
Source	vibrio cholerae rc385 (bacteria) synthetic construct (others) lama glama (llama) staphylococcus capitis (bacteria) homo sapiens (human)
Keywords	MEMBRANE PROTEIN / NabFab / anti-nanobody Fab / fiducial / NorM / MATE / DMT / IMMUNE SYSTEM / Antigen / FAB / Single-Domain Antibody