Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX
Ghanbarpour, A., Sauer, R.T., Davis, J.H.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
ATP-dependent Clp protease ATP-binding subunit ClpX | 389 | Escherichia coli | Mutation(s): 0  Gene Names: clpX, lopC, b0438, JW0428 | ||
UniProt | |||||
Find proteins for P0A6H1 (Escherichia coli (strain K12)) Explore P0A6H1  Go to UniProtKB:  P0A6H1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0A6H1 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Dihydrofolate reductase | G [auth S] | 210 | Escherichia coli | Mutation(s): 0  Gene Names: folA, HmCmsJML131_03510 EC: 1.5.1.3 | |
UniProt | |||||
Find proteins for A0A4C7B7M9 (Escherichia coli) Explore A0A4C7B7M9  Go to UniProtKB:  A0A4C7B7M9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A4C7B7M9 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
ATP-dependent Clp protease proteolytic subunit | 207 | Escherichia coli | Mutation(s): 0  Gene Names: clpP, lopP, b0437, JW0427 EC: 3.4.21.92 | ||
UniProt | |||||
Find proteins for P0A6G7 (Escherichia coli (strain K12)) Explore P0A6G7  Go to UniProtKB:  P0A6G7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0A6G7 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 4 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ATP (Subject of Investigation/LOI) Query on ATP | V [auth A], X [auth B], Z [auth C] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N | |||
MTX (Subject of Investigation/LOI) Query on MTX | FA [auth S] | METHOTREXATE C20 H22 N8 O5 FBOZXECLQNJBKD-ZDUSSCGKSA-N | |||
ADP (Subject of Investigation/LOI) Query on ADP | BA [auth D], DA [auth E], EA [auth F] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N | |||
MG (Subject of Investigation/LOI) Query on MG | AA [auth C], CA [auth D], W [auth A], Y [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Task | Software Package | Version |
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MODEL REFINEMENT | PHENIX | 1.14_3260: |
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) | United States | R01-GM144542 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R35-GM141517 |
National Science Foundation (NSF, United States) | United States | 2046778 |