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6z3r

Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ

Method: ELECTRON MICROSCOPY Dmax: 169.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

;Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1 ;

Homo sapiens

UniProt Q96Q15

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 259–1638 Chain A； UniProt 1727–2056 Chain A； UniProt 2088–3661 Not recorded Protein SMG8 × 1 （Q8ND04） Protein SMG9 × 1 （Q9H0W8） Regulator of nonsense transcripts 1 × 1 （Q92900） ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 2.97 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6Z3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6L53 Structure of SMG1 Deposited 2019-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–3661（3661 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å
6L54 Structure of SMG189 Deposited 2019-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–3661（3661 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
6SYT Structure of the SMG1-SMG8-SMG9 complex Deposited 2019-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–2232（145 aa）
Chain A 2275–3661（1387 aa）
Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；PBS
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.45 Å
7PW4 Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
7PW5 Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1 inhibitor Deposited 2021-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
7PW6 Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor - SMG1 body Deposited 2021-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 766–1638（873 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.05 Å
7PW7 Human SMG1-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.59 Å
7PW8 Human SMG1-8-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 1895–1916（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.82 Å
7PW9 Human SMG1-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.12 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMG1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 70–1449； UniProt 259–1638 Author chain A； PDBConstruct 1492–1821； UniProt 1727–2056 Author chain A； PDBConstruct 1838–3411； UniProt 2088–3661

Protein SMG8

Homo sapiens

UniProt Q8ND04

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–991 Not recorded ;Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1 ; × 1 （Q96Q15） Protein SMG9 × 1 （Q9H0W8） Regulator of nonsense transcripts 1 × 1 （Q92900） ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 2.97 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6Z3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6L54 Structure of SMG189 Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
6SYT Structure of the SMG1-SMG8-SMG9 complex Deposited 2019-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；PBS
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.45 Å
7PW4 Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
7PW5 Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1 inhibitor Deposited 2021-10-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
7PW8 Human SMG1-8-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.82 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMG8_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–991； UniProt 1–991

Protein SMG9

Homo sapiens

UniProt Q9H0W8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–520 Not recorded ;Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1 ; × 1 （Q96Q15） Protein SMG8 × 1 （Q8ND04） Regulator of nonsense transcripts 1 × 1 （Q92900） ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 2.97 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6Z3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6L54 Structure of SMG189 Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
6SYT Structure of the SMG1-SMG8-SMG9 complex Deposited 2019-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；PBS
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.45 Å
7PW4 Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
7PW5 Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1 inhibitor Deposited 2021-10-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
7PW7 Human SMG1-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.59 Å
7PW8 Human SMG1-8-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.82 Å
7PW9 Human SMG1-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 169–520（352 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.12 Å
8FE7 Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 140–151（12 aa）
Not recorded UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol
Resolution 2.98 Å R-free 0.217
8FE7 Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 140–151（12 aa）
Not recorded UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol
Resolution 2.98 Å R-free 0.217
8FE7 Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 140–151（12 aa）
Not recorded UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol
Resolution 2.98 Å R-free 0.217
8FE7 Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 140–151（12 aa）
Not recorded UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol
Resolution 2.98 Å R-free 0.217

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMG9_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–520； UniProt 1–520

Regulator of nonsense transcripts 1

OrganismNot specified

UniProt Q92900

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 1085–1095 Not recorded ;Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1 ; × 1 （Q96Q15） Protein SMG8 × 1 （Q8ND04） Protein SMG9 × 1 （Q9H0W8） ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 2.97 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6Z3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2GJK Structural and functional insights into the human Upf1 helicase core Deposited 2006-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 295–914（620 aa） Fragment：helicase core domain(residues 295-914)
Not recorded MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6；295 K；50mM MES, 0.5-3% PEG4000, 0.005mM MgSO4, 10mM DTT, pH 6.0, EVAPORATION, temperature 295K
Resolution 2.60 Å R-free 0.271
2GK6 Structural and Functional insights into the human Upf1 helicase core Deposited 2006-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 295–914（620 aa） Fragment：helicase core domain(residues 295-914)
Not recorded MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；295 K；100mM Tris, 8-13% PEG3350, 140mM (NH4)3PO4, 10% EG, 10mM DTT, pH 7.5, EVAPORATION, temperature 295K
Resolution 2.40 Å R-free 0.272
2GK6 Structural and Functional insights into the human Upf1 helicase core Deposited 2006-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 295–914（620 aa） Fragment：helicase core domain(residues 295-914)
Not recorded MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；295 K；100mM Tris, 8-13% PEG3350, 140mM (NH4)3PO4, 10% EG, 10mM DTT, pH 7.5, EVAPORATION, temperature 295K
Resolution 2.40 Å R-free 0.272
2GK7 Structural and Functional insights into the human Upf1 helicase core Deposited 2006-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 295–914（620 aa） Fragment：helicase core domain(residues 295-914)
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.8；295 K；100mM Na/K Phosphate, 6-8% PEG3350, 10mM DTT, pH 5.8, EVAPORATION, temperature 295K
Resolution 2.80 Å R-free 0.298
2IYK Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1 Deposited 2006-07-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 115–272（158 aa） Fragment：UPF2-INTERACTING DOMAIN, RESIDUES 115-272
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；30% PENTAERYTHRITOL ETHOXYLATE (15/4EO/OH) (V/V), 50 MM AMMONIUM SULPHATE,50 MM BIS-TRIS PH 6.5
Resolution 2.95 Å R-free 0.259
2IYK Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1 Deposited 2006-07-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 115–272（158 aa） Fragment：UPF2-INTERACTING DOMAIN, RESIDUES 115-272
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；30% PENTAERYTHRITOL ETHOXYLATE (15/4EO/OH) (V/V), 50 MM AMMONIUM SULPHATE,50 MM BIS-TRIS PH 6.5
Resolution 2.95 Å R-free 0.259
2WJV Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Deposited 2009-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 115–914（800 aa） Fragment：CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.5-1.6M AMMONIUM SULPHATE, 100 MM MES PH 6.3-6.5 AND 2% V/V GLYCEROL
Resolution 2.85 Å R-free 0.248
2WJV Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Deposited 2009-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 115–914（800 aa） Fragment：CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；1.5-1.6M AMMONIUM SULPHATE, 100 MM MES PH 6.3-6.5 AND 2% V/V GLYCEROL
Resolution 2.85 Å R-free 0.248
2WJY Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Orthorhombic form Deposited 2009-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 115–914（800 aa） Fragment：CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.6M AMMONIUM SULPHATE, 100 MM MES PH 6, 10% DIOXANE
Resolution 2.50 Å R-free 0.240
2XZO Upf1 helicase - RNA complex Deposited 2010-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 295–914（620 aa） Fragment：HELICASE DOMAIN, RESIDUES 295-914
Not recorded 1PE PENTAETHYLENE GLYCOL × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；100 MM SODIUM ACETATE PH 4.6, 20 MM CACL2, 15% MPD
Resolution 2.40 Å R-free 0.233
2XZP Upf1 helicase Deposited 2010-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 295–914（620 aa） Fragment：HELICASE DOMAIN, RESIDUES 295-914
Not recorded GOL GLYCEROL × 9 MLI MALONATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；50MM SODIUM CITRATE PH 6.0, 1.5M SODIUM MALONATE
Resolution 2.72 Å R-free 0.214
6EJ5 A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner Deposited 2017-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 295–925（631 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；291 K；1.4 M sodium malonate, 50 mM sodium citrate pH 6.2
Resolution 3.34 Å R-free 0.309
8RXB Human UPF1 CH domain in complex with SMG6 peptide Deposited 2024-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 115–287（173 aa）
Chain D 115–287（173 aa）
Chain E 115–287（173 aa）
Chain I 115–287（173 aa）
Chain L 115–287（173 aa）
Chain P 115–287（173 aa）
Not recorded ZN ZINC ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；solution (28% (w/v) PEG 3500, 0.2M Lithium sulfate and 0.1 M Tris pH 7.8)
Resolution 2.60 Å R-free 0.295
9QWN Human UPF1 in complex with the histone stem loop RNA Deposited 2025-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 115–914（800 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RENT1_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–11； UniProt 1085–1095

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6z3r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6z3r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6z3r
Deposition date deposition_date2020-05-21
Structure title titleStructure of SMG1-8-9 kinase complex bound to UPF1-LSQ
Keywords keywordsCryo-EM, Structural Biology, Nonsense-mediated mRNA decay, RNA quality control, PIKK, NMD, Substrate, Phosphorylation, TRANSFERASE; TRANSFERASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.16 Å
Radius of gyration Rg (electron density) rg_electron49.44 Å
Forward intensity I(0) i01017530000.00
Molecular weight molecular_weight269090.0 kDa
Excluded volume excluded_volume338390 ų
Envelope volume envelope_volume531600 ų
Hydration-shell volume shell_volume87563 ų
Envelope diameter envelope_diameter178.1 Å
Shell Rg shell_rg54.47 Å
Envelope Rg envelope_rg49.83 Å
Shape Rg shape_rg49.54 Å
Total Rg total_rg49.28 Å
Total atoms total_atoms36011
Residues n_residues2636
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax169.4 Å
Rg (real space) rg_real50.19 Å
Rg uncertainty (real space) rg_real_error1.64 Å
I(0) (real space) i0_real1.0180e+09
I(0) uncertainty (real space) i0_real_error2.0670e+07
Rg (reciprocal space) rg_reciprocal50.14 Å
I(0) (reciprocal space) i0_reciprocal1017000000.0000
Solution quality estimate total_estimate0.8775
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary60.1 Å
Skewness Skewness skewness0.356
Kurtosis Kurtosis kurtosis-0.363
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha110200000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.817
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)