28QN | pdb_000028qn

MBP-maltose bound to distal DARPin (AHIR dodecamer scaffold system)

PDB DOI: https://doi.org/10.2210/pdb28QN/pdb
EM Map EMD-56751: EMDB EMDataResource

Classification: SUGAR BINDING PROTEIN
Organism(s): synthetic construct, Methanosarcina mazei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-02-13 Released: 2026-02-25
Deposition Author(s): Ferreira, D.S.M., Noble, M., Rowland, R.J., Fairhead, M., Gittins, O., von Delft, F., Endicott, J., Martin, M., Pike, A.C.W., Sauer, D.B., Dlamini, L.S.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

An engineered symmetrical scaffold system enables high resolution imaging of small cargo proteins by cryo-electron microscopy

Ferreira, D.S.M., Noble, M., Rowland, R.J., Gittins, O., Martin, M., Endicott, J., Fairhead, M., von Delft, F., Pike, A.C.W., Sauer, D.B., Dlamini, L.S.

To be published.

Macromolecule Content

Total Structure Weight: 58.78 kDa
Atom Count: 4,084
Modeled Residue Count: 534
Deposited Residue Count: 534
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin	A	160	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein	B [auth C]	374	Methanosarcina mazei	Mutation(s): 0 Gene Names: malE, DU74_04045
UniProt
Find proteins for A0A0F8NYV9 (Methanosarcina mazei) Explore A0A0F8NYV9 Go to UniProtKB: A0A0F8NYV9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F8NYV9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C [auth B]	2		N/A	Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	C [auth B]	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T003677/1

Revision History (Full details and data files)

Version 1.0: 2026-02-25
Type: Initial release
Version 2.0: 2026-03-18
Type: Coordinate replacement
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary