Resolution: 5.67 Å
EM Method: Single-particle
Fitted PDBs: 8ez9
Q-score: 0.074
Chen S, Vogt A, Lee L, Naila T, McKeown R, Tomkinson AE, Lees-Miller SP, He Y
Sci Adv (2023) 9 pp. eadg2838-eadg2838 [ Pubmed: 37256947 DOI: doi:10.1126/sciadv.adg2838 ]
- Unknown region of dna-pkcs (1 kDa, Protein from Homo sapiens)
- Dimer of dna-pkcs (940 kDa, Complex from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
NHEJ Long-range complex with PAXX
Resolution: 4.39 Å
EM Method: Single-particle
Fitted PDBs: 8eza
Q-score: 0.216
Chen S, Vogt A, Lee L, Naila T, McKeown R, Tomkinson AE, Lees-Miller SP, He Y
Sci Adv (2023) 9 pp. eadg2838-eadg2838 [ Pubmed: 37256947 DOI: doi:10.1126/sciadv.adg2838 ]
- Nhej long-range complex with paxx (1 MDa, Complex)
- Dna (31-mer) (9 kDa, DNA from Homo sapiens)
- Prkdc_human dna-dependent protein kinase catalytic subunit -- unknown region (1 kDa, Protein from Homo sapiens)
- Dna (30-mer) (9 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Protein paxx (21 kDa, Protein from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
NHEJ Long-range complex with ATP
Resolution: 8.9 Å
EM Method: Single-particle
Fitted PDBs: 8ezb
Q-score: 0.08
Chen S, Vogt A, Lee L, Naila T, McKeown R, Tomkinson AE, Lees-Miller SP, He Y
Sci Adv (2023) 9 pp. eadg2838-eadg2838 [ Pubmed: 37256947 DOI: doi:10.1126/sciadv.adg2838 ]
- Dna (31-mer) (9 kDa, DNA from Homo sapiens)
- Dna (30-mer) (9 kDa, DNA from Homo sapiens)
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Non-homologous end-joining factor 1 (33 kDa, Protein from Homo sapiens)
- Nhej long-range complex with atp (1 MDa, Complex)
- Dna ligase 4 (104 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Protein paxx (21 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna repair protein xrcc4 (38 kDa, Protein from Homo sapiens)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
Structure of ACLY-D1026A-substrates
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 7rig
Q-score: 0.588
Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R
Nat Commun (2023) 14 pp. 2247-2247 [ Pubmed: 37076498 DOI: doi:10.1038/s41467-023-37986-9 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Acly d1026a mutant in complex with coa and citrate (480 kDa, Complex from Homo sapiens)
- Phosphate ion (94 Da, Ligand)
- Atp-citrate synthase (120 kDa, Protein from Homo sapiens)
- (3s)-citryl-coenzyme a (941 Da, Ligand)
- Unknown ligand (189 Da, Ligand)
- Coenzyme a (767 Da, Ligand)
- Citrate anion (189 Da, Ligand)
- Water (18 Da, Ligand)
Structure of ACLY D1026A-substrates-asym-int
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7rkz
Q-score: 0.412
Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R
Nat Commun (2023) 14 pp. 2247-2247 [ Pubmed: 37076498 DOI: doi:10.1038/s41467-023-37986-9 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Acly d1026a mutant in complex with coa and citrate (480 kDa, Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Atp-citrate synthase (120 kDa, Protein from Homo sapiens)
- (3s)-citryl-coenzyme a (941 Da, Ligand)
- Coenzyme a (767 Da, Ligand)
- Citrate anion (189 Da, Ligand)
- Unknown ligand (767 Da, Ligand)
Structure of ACLY D1026A - substrates-asym
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7rmp
Q-score: 0.427
Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R
Nat Commun (2023) 14 pp. 2247-2247 [ Pubmed: 37076498 DOI: doi:10.1038/s41467-023-37986-9 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Acly d1026a mutant in complex with coa and citrate (480 kDa, Complex from Homo sapiens)
- Phosphate ion (94 Da, Ligand)
- Water (18 Da, Ligand)
- Atp-citrate synthase (120 kDa, Protein from Homo sapiens)
- (3s)-citryl-coenzyme a (941 Da, Ligand)
- Coenzyme a (767 Da, Ligand)
- Citrate anion (189 Da, Ligand)
- Unknown ligand (767 Da, Ligand)
Structure of ACLY-D1026A-products-asym
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8g1e
Q-score: 0.424
Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R
Nat Commun (2023) 14 pp. 2247-2247 [ Pubmed: 37076498 DOI: doi:10.1038/s41467-023-37986-9 ]
- Phosphate ion (94 Da, Ligand)
- Acly d1026a mutant in complex with coa and citrate (480 kDa, Complex from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp-citrate synthase (120 kDa, Protein from Homo sapiens)
- (3s)-citryl-coenzyme a (941 Da, Ligand)
- Acetyl coenzyme *a (809 Da, Ligand)
- Oxaloacetate ion (131 Da, Ligand)
- Unknown ligand (Ligand)
- Water (18 Da, Ligand)
Structure of ACLY-D1026A-products
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8g1f
Q-score: 0.581
Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R
Nat Commun (2023) 14 pp. 2247-2247 [ Pubmed: 37076498 DOI: doi:10.1038/s41467-023-37986-9 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
- Atp-citrate synthase (120 kDa, Protein from Homo sapiens)
- (3s)-citryl-coenzyme a (941 Da, Ligand)
- Acly d1026a mutant in complex with products (480 kDa, Complex from Homo sapiens)
- Acetyl coenzyme *a (809 Da, Ligand)
- Oxaloacetate ion (131 Da, Ligand)
- Unknown ligand (Ligand)
- Water (18 Da, Ligand)
Structure of ACLY-D1026A-substrates, local refinement of ASH domain
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8g5c
Q-score: 0.635
Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R
Nat Commun (2023) 14 pp. 2247-2247 [ Pubmed: 37076498 DOI: doi:10.1038/s41467-023-37986-9 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Acly d1026a mutant in complex with coa and citrate (480 kDa, Complex from Homo sapiens)
- Phosphate ion (94 Da, Ligand)
- Atp-citrate synthase (120 kDa, Protein from Homo sapiens)
- (3s)-citryl-coenzyme a (941 Da, Ligand)
- Coenzyme a (767 Da, Ligand)
- Citrate anion (189 Da, Ligand)
- Water (18 Da, Ligand)
Structure of ACLY-D1026A-products, local refinement of ASH domain
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8g5d
Q-score: 0.631
Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R
Nat Commun (2023) 14 pp. 2247-2247 [ Pubmed: 37076498 DOI: doi:10.1038/s41467-023-37986-9 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
- Atp-citrate synthase (120 kDa, Protein from Homo sapiens)
- Acly d1026a mutant in complex with acetyl-coa and oaa (480 kDa, Complex from Homo sapiens)
- (3s)-citryl-coenzyme a (941 Da, Ligand)
- Acetyl coenzyme *a (809 Da, Ligand)
- Oxaloacetate ion (131 Da, Ligand)
- Water (18 Da, Ligand)