6K1H

Structure of membrane protein

PDB DOI: https://doi.org/10.2210/pdb6K1H/pdb
EM Map EMD-9906: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Escherichia coli str. K-12 substr. MG1655, Escherichia coli K-12
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2019-05-10 Released: 2019-07-10
Deposition Author(s): Wang, J.W., Zeng, J.W.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.52 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structure of the mannose transporter of the bacterial phosphotransferase system.

Liu, X., Zeng, J., Huang, K., Wang, J.

(2019) Cell Res 29: 680-682

PubMed: 31209249 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-019-0194-z
Primary Citation of Related Structures:
6K1H

Organizational Affiliation

State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China.

Macromolecule Content

Total Structure Weight: 179.75 kDa
Atom Count: 11,769
Modelled Residue Count: 1,560
Deposited Residue Count: 1,671
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS mannose transporter subunit IID	A [auth Z], C [auth F], E [auth C]	283	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0 Gene Names: D8B36_09735 Membrane Entity: Yes
UniProt
Find proteins for P69805 (Escherichia coli (strain K12)) Explore P69805 Go to UniProtKB: P69805
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69805
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system mannose-specific EIIC component	B [auth Y], D [auth E], F [auth B]	274	Escherichia coli K-12	Mutation(s): 0 Gene Names: manY, pel, ptsP, b1818, JW1807 Membrane Entity: Yes
UniProt
Find proteins for P69801 (Escherichia coli (strain K12)) Explore P69801 Go to UniProtKB: P69801
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69801
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN (Subject of Investigation/LOI) Query on MAN Download Ideal Coordinates CCD File SDF format, chain G [auth Z] SDF format, chain H [auth F] SDF format, chain I [auth C] MOL2 format, chain G [auth Z] MOL2 format, chain H [auth F] MOL2 format, chain I [auth C] mmCIF format, chain G [auth Z] mmCIF format, chain H [auth F] mmCIF format, chain I [auth C]	G [auth Z], H [auth F], I [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain G [auth Z] Focus chain H [auth F] Focus chain I [auth C] Interactions & Density Focus chain G [auth Z] Focus chain H [auth F] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.52 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-10

Deposition Author(s):

Wang, J.W.

Zeng, J.W.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	No. 2016YFA0501103
Ministry of Science and Technology (MoST, China)	China	2015CB910104
National Natural Science Foundation of China (NSFC)	China	31621092

Revision History (Full details and data files)

Version 1.0: 2019-07-10
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Database references
Version 1.2: 2019-08-14
Changes: Data collection, Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.0: 2020-09-16
Type: Coordinate replacement
Reason: Model orientation/position
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2024-03-27
Changes: Data collection, Database references