1c8c

CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS

Method: X-RAY DIFFRACTION D_max: 46.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-BINDING PROTEIN 7A

OrganismNot specified

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–64	Not recorded	5'-D(GPTPGPAPTPCPGPC)-3' × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 1.3MM SSO7D, 1.3MM DUPLEX DNA, 2.5 MM TRIS (PH 6.5), 2.5% PEG 400, EQUILIBRATED AGAINST 15% PEG 400 at pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 1.45 Å R-free 0.287

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 1C8C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BBX NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE Deposited 1998-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 1–63（63 aa） Chain D 1–63（63 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；323 K；Ionic strength (raw mmCIF value) 60 mM；Pressure 1 NMR sample composition H2O:D2O 9:1	Resolution not provided
1JIC SOLUTION NMR STRUCTURE OF RECOMBINANT SSO7D WITH RNASE ACTIVITY, MINIMIZED AVERAGE STRUCTURE Deposited 1998-07-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–62（62 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；300 K NMR sample composition H2O	Resolution not provided
5B02 Structure of the prenyltransferase MoeN5 with a fusion protein tag of Sso7d Deposited 2015-10-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350	Resolution 2.21 Å R-free 0.218
5B02 Structure of the prenyltransferase MoeN5 with a fusion protein tag of Sso7d Deposited 2015-10-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350	Resolution 2.21 Å R-free 0.218
5B03 Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate Deposited 2015-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	GPP GERANYL DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5mM GPP, 0.3M Li3-citrate, 0.4M NaCl, 27% PEG 3350, 5% glycerol	Resolution 2.60 Å R-free 0.239
5B03 Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate Deposited 2015-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	GPP GERANYL DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5mM GPP, 0.3M Li3-citrate, 0.4M NaCl, 27% PEG 3350, 5% glycerol	Resolution 2.60 Å R-free 0.239
5B0I Structure of MoeN5-Sso7d fusion protein in complex with beta-octyl glucoside Deposited 2015-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	BOG octyl beta-D-glucopyranoside × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5% Glycerol, 1% beta-octyl glucoside	Resolution 2.26 Å R-free 0.229
5B0I Structure of MoeN5-Sso7d fusion protein in complex with beta-octyl glucoside Deposited 2015-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	BOG octyl beta-D-glucopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5% Glycerol, 1% beta-octyl glucoside	Resolution 2.26 Å R-free 0.229
5B0J Structure of MoeN5-Sso7d fusion protein in complex with beta-undecyl maltoside Deposited 2015-10-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% undecylmaltoside	Resolution 2.50 Å R-free 0.238
5B0J Structure of MoeN5-Sso7d fusion protein in complex with beta-undecyl maltoside Deposited 2015-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	UMQ UNDECYL-MALTOSIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% undecylmaltoside	Resolution 2.50 Å R-free 0.238
5B0K Structure of MoeN5-Sso7d fusion protein in complex with beta-decyl maltoside Deposited 2015-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5% glycerol, 1% beta-decyl-D-maltoside	Resolution 2.75 Å R-free 0.248
5B0K Structure of MoeN5-Sso7d fusion protein in complex with beta-decyl maltoside Deposited 2015-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 5% glycerol, 1% beta-decyl-D-maltoside	Resolution 2.75 Å R-free 0.248
5B0L Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	BNG nonyl beta-D-glucopyranoside × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside	Resolution 2.80 Å R-free 0.232
5B0L Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	BNG nonyl beta-D-glucopyranoside × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside	Resolution 2.80 Å R-free 0.232
5B0L Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–64（64 aa） Chain F 1–64（64 aa）	Not recorded	BNG nonyl beta-D-glucopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside	Resolution 2.80 Å R-free 0.232
5B0L Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–64（64 aa） Chain H 1–64（64 aa）	Not recorded	BNG nonyl beta-D-glucopyranoside × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-nonyl-D-glucoside	Resolution 2.80 Å R-free 0.232
5B0M Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-dodecyl-D-maltoside	Resolution 3.05 Å R-free 0.249
5B0M Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-dodecyl-D-maltoside	Resolution 3.05 Å R-free 0.249
5B0M Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–64（64 aa） Chain F 1–64（64 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-dodecyl-D-maltoside	Resolution 3.05 Å R-free 0.249
5B0M Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–64（64 aa） Chain H 1–64（64 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M Li3-citrate, 0.3M NaCl, 25% PEG 3350, 1% beta-dodecyl-D-maltoside	Resolution 3.05 Å R-free 0.249
5GWV Structure of MoeN5-Sso7d fusion protein in complex with a substrate analogue Deposited 2016-09-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；Protein: 10mg/mL in 10mM DTT, 1mM MgCl2 Reservoir: 0.2M Li3-citrate, 0.3M NaCl, 25% w/v PEG 3350 Cryoprotectant: 5mM substrate analogue in 0.3M Li3-citrate, 0.4M NaCl, 27% w/v PEG 3350, 5% glycerol	Resolution 2.40 Å R-free 0.216
5GWV Structure of MoeN5-Sso7d fusion protein in complex with a substrate analogue Deposited 2016-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	78S (2R)-3-dimethoxyphosphoryloxy-2-[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；Protein: 10mg/mL in 10mM DTT, 1mM MgCl2 Reservoir: 0.2M Li3-citrate, 0.3M NaCl, 25% w/v PEG 3350 Cryoprotectant: 5mM substrate analogue in 0.3M Li3-citrate, 0.4M NaCl, 27% w/v PEG 3350, 5% glycerol	Resolution 2.40 Å R-free 0.216
5GWW Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue Deposited 2016-09-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；protein: 10 mg/mL in 10 mM DTT, 1 mM MgCl2 reservoir: 0.2 M Li3 citrate, 0.3 M NaCl, 25% w/v PEG 3350 cryoprotectant: 5 mM permethylated analogue, 0.3 M Li3 citrate, 0.4 M NaCl, 27% w/v PEG 3350, 5% glycerol	Resolution 2.30 Å R-free 0.221
5GWW Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue Deposited 2016-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	7B5 methyl (2R)-3-dimethoxyphosphoryloxy-2-[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；protein: 10 mg/mL in 10 mM DTT, 1 mM MgCl2 reservoir: 0.2 M Li3 citrate, 0.3 M NaCl, 25% w/v PEG 3350 cryoprotectant: 5 mM permethylated analogue, 0.3 M Li3 citrate, 0.4 M NaCl, 27% w/v PEG 3350, 5% glycerol	Resolution 2.30 Å R-free 0.221
6J8V Structure of MOEN5-SSO7D fusion protein in complex with ligand 2 Deposited 2019-01-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350	Resolution 2.23 Å R-free 0.225
6J8V Structure of MOEN5-SSO7D fusion protein in complex with ligand 2 Deposited 2019-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	FAR FARNESYL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350	Resolution 2.23 Å R-free 0.225
6J8W Structure of MOEN5-SSO7D fusion protein in complex with lig 1 Deposited 2019-01-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa） Chain B 1–64（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350	Resolution 2.35 Å R-free 0.225
6J8W Structure of MOEN5-SSO7D fusion protein in complex with lig 1 Deposited 2019-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	C0X (2S)-3-dimethoxyphosphoryloxy-2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298 K；0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350	Resolution 2.35 Å R-free 0.225
6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	CA CALCIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å R-free 0.536
6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å R-free 0.536
6PUT Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å R-free 0.536
6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 4 ZN ZINC ION × 4 KLQ Bictegravir × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å R-free 0.534
6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 KLQ Bictegravir × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å R-free 0.534
6PUW Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 KLQ Bictegravir × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å R-free 0.534
6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 4 ZN ZINC ION × 4 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å R-free 0.516
6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å R-free 0.516
6PUY Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 OZ1 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å R-free 0.516
6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 4 ZN ZINC ION × 4 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å R-free 0.535
6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å R-free 0.535
6PUZ Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f) Deposited 2019-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 XXJ 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å R-free 0.535
6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 4 ZN ZINC ION × 4 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å R-free 0.555
6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å R-free 0.555
6V3K Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c) Deposited 2019-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 2 QUW 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å R-free 0.555
6VOY Cryo-EM structure of HTLV-1 instasome Deposited 2020-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: dodecameric	Chain A 1–64（64 aa） Chain B 1–64（64 aa） Chain C 1–64（64 aa） Chain D 1–64（64 aa）	Mutation：W24A Mutation：W24A Mutation：W24A Mutation：W24A	ZN ZINC ION × 4 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.70 Å

19 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DN72_SULSO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–64； UniProt 1–64

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c8c
Deposition date deposition_date	2000-05-04
Structure title title	CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS
Keywords keywords	;DNA BINDING PROTEIN, PROTEIN-DNA INTERACTION, PROTEIN STABILITY, HYPERTHERMOPHILE, ACHAEABACTERIA, ELECTROSTATICS, MOLECULAR MODELING, T-G MISMATCH, DNA BINDING PROTEIN-DNA COMPLEX ;; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.38 Å
Radius of gyration Rg (electron density) rg_electron	13.29 Å
Forward intensity I(0) i0	4317230.00
Molecular weight molecular_weight	12092.0 kDa
Excluded volume excluded_volume	13965 Å³
Envelope volume envelope_volume	16949 Å³
Hydration-shell volume shell_volume	10956 Å³
Envelope diameter envelope_diameter	47.9 Å
Shell Rg shell_rg	18.91 Å
Envelope Rg envelope_rg	13.74 Å
Shape Rg shape_rg	13.20 Å
Total Rg total_rg	14.54 Å
Total atoms total_atoms	998
Residues n_residues	80
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	46.3 Å
Rg (real space) rg_real	14.31 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	4.3170e+06
I(0) uncertainty (real space) i0_real_error	4.9120e+04
Rg (reciprocal space) rg_reciprocal	14.32 Å
I(0) (reciprocal space) i0_reciprocal	4317000.0000
Solution quality estimate total_estimate	0.8102
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.2 Å
Skewness Skewness skewness	0.202
Kurtosis Kurtosis kurtosis	-0.278
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	445500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	5'-D(GPTPGPAPTPCPGPC)-3'
Molecular weight formula_weight	2442.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C
Atom count atom_count	1469

GTGATCGC

Entity 2 Entity 2 polymer

Description description	DNA-BINDING PROTEIN 7A
Molecular weight formula_weight	7236.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MATVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLAKQKK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c8ca_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.1 — Histone-like proteins from archaea

CATH v4.4 (1 domains)

Domain ID domain_id	1c8cA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	47.475 Å
Unit-cell length b length_b	49.800 Å
Unit-cell length c length_c	37.681 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2290
R_work r_work	—
R_free r_free	0.2868

fit	/app/data/saxs_computation/c8/1c8c/1c8c.fit
pddf	/app/data/pr_computation/c8/1c8c/1c8c.pr.out
profile	/app/data/saxs_computation/c8/1c8c/1c8c.dat

CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-BINDING PROTEIN 7A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)