9AXW | pdb_00009axw

Nanobody NbJRI bound to yeast Pdc1

PDB DOI: https://doi.org/10.2210/pdb9AXW/pdb

Classification: IMMUNE SYSTEM
Organism(s): Saccharomyces cerevisiae, Vicugna pacos
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-06 Released: 2026-03-25
Deposition Author(s): Carrasco-Lopez, C., Avalos, J.L.
Funding Organization(s): Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Nanobody-mediated inhibition of yeast pyruvate decarboxylase by active site denaturation

Carrasco-Lopez, C., Gonzalez, C.L., Avalos, J.L.

To be published.

Macromolecule Content

Total Structure Weight: 635.37 kDa
Atom Count: 39,941
Modeled Residue Count: 5,199
Deposited Residue Count: 5,800
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
branched-chain-2-oxoacid decarboxylase	A [auth AA1] B [auth BA1] C [auth CA1] D [auth DA1] E [auth EA1] A [auth AA1], B [auth BA1], C [auth CA1], D [auth DA1], E [auth EA1], F [auth FA1], G [auth GA1], H [auth HA1]	573	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PDC1, GI527_G0003862 EC: 4.1.1.72

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NbJRi	I J K L M [auth N] I, J, K, L, M [auth N], N [auth O], O [auth P], P [auth M]	152	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.449	α = 79.42
b = 113.048	β = 78.06
c = 155.496	γ = 67.02

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
BALBES	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Carrasco-Lopez, C.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0019363
Department of Energy (DOE, United States)	United States	DE-SC0022155
National Science Foundation (NSF, United States)	United States	CBET-1751840

Revision History (Full details and data files)

Version 1.0: 2026-03-25
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.