4a8b Summary

pdbe.org/4a8b
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Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozymes

The structure was published by Malet, H., Canellas, F., Sawa, J., et al., Ehrmann, M., Clausen, T., and Saibil, H.R., in 2012 in a paper entitled "Newly Folded Substrates Inside the Molecular Cage of the Htra Chaperone Degq" (abstract).

The structure was determined using Electron microscopy at a resolution of 13.0 Å and deposited in 2011.

The experimental data on which the structure is based was deposited separately in EMDB as entry 1982.

This PDB entry contains a complex of 2 biomacromolecules, namely PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ and LYSOZYME C.

The most likely quaternary structure is a 18meric assembly.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
B PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
C PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
D PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
E PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
F PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
G PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
H PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
I PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
J PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
K PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
L PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ P39099 (28-455) (DEGQ_ECOLI)search Escherichia coli K-12search 100% 436 88%
M LYSOZYME C P00698 (19-147) (LYSC_CHICK)search Gallus gallussearch 93% 129 100%
N LYSOZYME C P00698 (19-147) (LYSC_CHICK)search Gallus gallussearch 93% 129 100%
O LYSOZYME C P00698 (19-147) (LYSC_CHICK)search Gallus gallussearch 93% 129 100%
P LYSOZYME C P00698 (19-147) (LYSC_CHICK)search Gallus gallussearch 93% 129 100%
Q LYSOZYME C P00698 (19-147) (LYSC_CHICK)search Gallus gallussearch 93% 129 100%
R LYSOZYME C P00698 (19-147) (LYSC_CHICK)search Gallus gallussearch 93% 129 100%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P39099 (28 - 455) PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ Escherichia coli K-12
P00698 (19 - 147) LYSOZYME C Gallus gallus

Chain Sequence family (Pfam)
A, B, C, D, E, F, G, H, I, J, K, L (P39099) PF00595: PDZ domain (Also known as DHR or GLGF)search, PF13365: Trypsin-like peptidase domainsearch
M, N, O, P, Q, R (P00698) PF00062: C-type lysozyme/alpha-lactalbumin familysearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A, B, C, D, E, F, G, H, I, J, K, L (P39099) peptidase activitysearch identical protein bindingsearch serine-type peptidase activitysearch serine-type endopeptidase activitysearch catalytic activitysearch hydrolase activitysearch proteolysis involved in cellular protein catabolic processsearch proteolysissearch response to stresssearch periplasmic spacesearch integral component of external side of plasma membranesearch
M, N, O, P, Q, R (P00698) protein bindingsearch hydrolase activitysearch lysozyme activitysearch identical protein bindingsearch hydrolase activity, acting on glycosyl bondssearch catalytic activitysearch cytolysissearch defense response to bacteriumsearch cell wall macromolecule catabolic processsearch metabolic processsearch retina homeostasissearch extracellular regionsearch extracellular spacesearch extracellular vesicular exosomesearch

Chain InterPro annotation
A, B, C, D, E, F, G, H, I, J, K, L PDZ domainsearch Peptidase S1Csearch Trypsin-like cysteine/serine peptidase domainsearch Peptidase S1C, Dosearch
M, N, O, P, Q, R Glycoside hydrolase, family 22, lysozymesearch Glycoside hydrolase, family 22search Glycoside hydrolase, family 22, conserved sitesearch Lysozyme-like domainsearch