RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

232,059 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Structure Author = "Zhu, X.F."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	Escherichia coli K-12 (6)
	Shigella flexneri (3)
	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (2)
	Staphylococcus epidermidis RP62A (2)
	Escherichia coli BL21(DE3) (1)

Taxonomy

Bacteria (13)

Experimental Method

	ELECTRON MICROSCOPY (9)
	X-RAY DIFFRACTION (4)

Polymer Entity Type

Protein (13)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (2)
	3.0 - 3.5 (5)
	3.5 - 4.0 (3)
	4.0 - 4.5 (1)

Release Date

	2015 - 2019 (5)
	2020 - 2024 (8)

Enzyme Classification Name

	Translocases (9)
	Transferases (2)

Membrane Protein Annotation

	MemProtMD (9)
	OPM (9)
	PDBTM (9)
	mpstruc (9)

Symmetry Type

	Asymmetric (12)
	Cyclic (1)

SCOP Classification

Alpha and beta proteins (a/b) (1)

AllSelected

1 to 13 of 13 Structures

Page 1 of 1

Sort by

Explore in 3D

5YJC	Download File View File

Structural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm6

Zhao, Y.Q., Gu, Y.J., Zhu, X.F., Cheng, W.

To be published

Released	2018-10-17
Method	X-RAY DIFFRACTION 2.007 Å
Organisms	Staphylococcus epidermidis RP62A
Macromolecule	Csm6 (protein)

Explore in 3D

5YJD	Download File View File

Structural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm3

Zhao, Y.Q., Gu, Y.J., Zhu, X.F., Cheng, W.

To be published

Released	2018-10-17
Method	X-RAY DIFFRACTION 2.26 Å
Organisms	Staphylococcus epidermidis RP62A
Macromolecule	Csm3 (protein)
Unique Ligands	CA

Explore in 3D

6S8G	Download File View File

Cryo-EM structure of LptB2FGC in complex with AMP-PNP

Tang, X.D., Chang, S.H., Luo, Q.H., Zhang, Z.Y., Qiao, W., Xu, C.H., Zhang, C.B., Niu, Y., Yang, W.X., Wang, T., Zhang, Z.B., Zhu, X.F., Dong, C.J., Zhang, X., Dong, H.H.

(2019) Nat Commun 10: 4175-4175

Released	2019-09-25
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Shigella flexneri
Macromolecule	Inner membrane protein yjgQ (protein) LPS export ABC transporter permease LptF (protein) Lipopolysaccharide ABC transporter, ATP-binding protein LptB (protein)
Unique Ligands	ANP, LMD

Explore in 3D

6S8H	Download File View File

Cryo-EM structure of LptB2FG in complex with LPS

Tang, X.D., Chang, S.H., Luo, Q.H., Zhang, Z.Y., Qiao, W., Xu, C.H., Zhang, C.B., Niu, Y., Yang, W.X., Wang, T., Zhang, Z.B., Zhu, X.F., Dong, C.J., Zhang, X., Dong, H.H.

(2019) Nat Commun 10: 4175-4175

Released	2019-09-25
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Shigella flexneri
Macromolecule	Inner membrane protein yjgQ (protein) Lipopolysaccharide ABC transporter, ATP-binding protein LptB (protein) Lipopolysaccharide export system permease protein LptF (protein)
Unique Ligands	DCQ, JSG, LMN, LMT

Explore in 3D

6S8N	Download File View File

Cryo-EM structure of LptB2FGC in complex with lipopolysaccharide

Tang, X.D., Chang, S.H., Luo, Q.H., Zhang, Z.Y., Qiao, W., Xu, C.H., Zhang, C.B., Niu, Y., Yang, W.X., Wang, T., Zhang, Z.B., Zhu, X.F., Dong, C.J., Zhang, X., Dong, H.H.

(2019) Nat Commun 10: 4175-4175

Released	2019-09-25
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Shigella flexneri
Macromolecule	Inner membrane protein yjgQ (protein) Lipopolysaccharide ABC transporter, ATP-binding protein LptB (protein) Lipopolysaccharide export system permease protein LptF (protein) Lipopolysaccharide export system protein LptC (protein)
Unique Ligands	DCQ, L0W, LMN, LMT

Explore in 3D

6Y6G	Download File View File

lipopolysaccharide outer core galactosyltransferase WaaB apo form

Zhang, Z.Y., Ashworth, G., Wang, Z.S., Zhu, X.F., Dong, C.J.

To be published

Released	2021-03-31
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Macromolecule	Lipopolysaccharide 1,6-galactosyltransferase (protein)

Explore in 3D

6Y6I	Download File View File

lipopolysaccharide outer core galactosyltransferase WaaB and UDP complex

Zhang, Z.Y., Ashworth, G., Wang, Z.S., Zhu, X.F., Dong, C.J.

To be published

Released	2021-03-31
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Macromolecule	Lipopolysaccharide 1,6-galactosyltransferase (protein)
Unique Ligands	UDP

Explore in 3D

7ARH	Download File View File

LolCDE in complex with lipoprotein

Tang, X.D., Chang, S.H., Zhang, K., Wang, T., Luo, Q.H., Qiao, W., Wang, C., Zhang, Z.B., Zhang, Z.Y., Zhu, X.F., Dong, C.J., Zhang, X., Dong, H.H.

(2021) Nat Struct Mol Biol 28: 347-355

Released	2021-04-07
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Escherichia coli K-12
Macromolecule	LPP (protein) Lipoprotein-releasing ABC transporter permease subunit LolC (protein) Lipoprotein-releasing system ATP-binding protein LolD (protein) Lipoprotein-releasing system transmembrane protein LolE (protein)
Unique Ligands	PLM, Z41

Explore in 3D

7ARI	Download File View File

LolCDE apo structure

Tang, X.D., Chang, S.H., Zhang, K., Wang, T., Luo, Q.H., Qiao, W., Wang, C., Zhang, Z.B., Zhang, Z.Y., Zhu, X.F., Dong, C.J., Zhang, X., Dong, H.H.

(2021) Nat Struct Mol Biol 28: 347-355

Released	2021-04-07
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Escherichia coli K-12
Macromolecule	Lipoprotein-releasing ABC transporter permease subunit LolC (protein) Lipoprotein-releasing system ATP-binding protein LolD (protein) Lipoprotein-releasing system transmembrane protein LolE (protein)

Explore in 3D

7ARJ	Download File View File

LolCDE in complex with lipoprotein and AMPPNP complex undimerized form

Tang, X.D., Chang, S.H., Zhang, K., Wang, T., Luo, Q.H., Qiao, W., Wang, C., Zhang, Z.B., Zhang, Z.Y., Zhu, X.F., Dong, C.J., Zhang, X., Dong, H.H.

(2021) Nat Struct Mol Biol 28: 347-355

Released	2021-04-07
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Escherichia coli K-12
Macromolecule	LPP (protein) Lipoprotein-releasing ABC transporter permease subunit LolC (protein) Lipoprotein-releasing system ATP-binding protein LolD (protein) Lipoprotein-releasing system transmembrane protein LolE (protein)
Unique Ligands	ANP, MG, PLM, Z41

Explore in 3D

7ARK	Download File View File

LolCDE in complex with AMP-PNP in the closed NBD state

Tang, X.D., Chang, S.H., Zhang, K., Wang, T., Luo, Q.H., Qiao, W., Wang, C., Zhang, Z.B., Zhang, Z.Y., Zhu, X.F., Dong, C.J., Zhang, X., Dong, H.H.

(2021) Nat Struct Mol Biol 28: 347-355

Released	2021-04-07
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Escherichia coli K-12
Macromolecule	Lipoprotein-releasing ABC transporter permease subunit LolC (protein) Lipoprotein-releasing system ATP-binding protein LolD (protein) Lipoprotein-releasing system transmembrane protein LolE (protein)
Unique Ligands	ANP, MG

Explore in 3D

7ARL	Download File View File

LolCDE in complex with lipoprotein and ADP

Tang, X.D., Chang, S.H., Zhang, K., Wang, T., Luo, Q.H., Qiao, W., Wang, C., Shen, C.R., Zhang, Z.B., Zhang, Z.Y., Zhu, X.F., Wei, X.W., Dong, C.J., Zhang, X., Dong, H.H.

(2021) Nat Struct Mol Biol 28: 347-355

Released	2021-04-07
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Escherichia coli K-12
Macromolecule	LPP (protein) Lipoprotein-releasing ABC transporter permease subunit LolC (protein) Lipoprotein-releasing system ATP-binding protein LolD (protein) Lipoprotein-releasing system transmembrane protein LolE (protein)
Unique Ligands	ADP, MG, PLM, Z41

Explore in 3D

7ARM	Download File View File

LolCDE in complex with lipoprotein and LolA

Tang, X.D., Chang, S.H., Zhang, K., Wang, T., Luo, Q.H., Qiao, W., Wang, C., Shen, C.R., Zhang, Z.B., Zhang, Z.Y., Zhu, X.F., Wei, X.W., Dong, C.J., Zhang, X., Dong, H.H.

(2021) Nat Struct Mol Biol 28: 347-355

Released	2021-04-07
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Escherichia coli BL21(DE3) Escherichia coli K-12
Macromolecule	LPP (protein) Lipoprotein-releasing ABC transporter permease subunit LolC (protein) Lipoprotein-releasing system ATP-binding protein LolD (protein) Lipoprotein-releasing system transmembrane protein LolE (protein) Outer-membrane lipoprotein carrier protein (protein)
Unique Ligands	PLM, Z41

1 to 13 of 13 Structures

Page 1 of 1

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

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.

All questions and comments will receive a response in a timely manner.

Use this form for questions about RCSB.org and RCSB PDB services.
Please attach a screenshot when reporting an issue, if possible.
To update/release your in-progress structure depositions:
access the OneDep Communication panel
For questions/corrections to specific PDB entries, including citation updates:
email deposit-help@mail.wwpdb.org

First Name

Last Name

Subject

Question, Comment, Feedback or Other

Attach File(s)
Use CTRL or Shift keys to select more than one file ( files max)

I agree to the Help Desk Privacy Policy

Optional: To help us learn more about our users, what is your:

Institution Type

Role

Main Research Interest

Thank you for providing your feedback! Someone will be in touch with you shortly. This window will automatically close in 5 seconds.

Apologies, our feedback server is currently unavailable and we are troubleshooting the issue. In the meantime, please copy and paste the below information into an email addressed to info@rcsb.org

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification