9ja6

Cryo-EM structure of Tdk1 tetramer complex

Method: ELECTRON MICROSCOPY D_max: 108.0 Å Quality: GOOD

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

Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G

Streptococcus sp. group G

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–129 Chain A； UniProt 220–357 Chain B； UniProt 1–129 Chain B； UniProt 220–357 Chain C； UniProt 1–129 Chain C； UniProt 220–357 Chain D； UniProt 1–129 Chain D； UniProt 220–357	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 4.40 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 9JA6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9JA5 Cryo-EM structure of Tdk1-Bdf1 complex Deposited 2024-08-24	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 211–357（147 aa） Chain B 211–357（147 aa） Chain C 211–357（147 aa） Chain D 211–357（147 aa） Chain E 211–357（147 aa） Chain F 211–357（147 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 2.70 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MU135_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–129； UniProt 1–129 Author chain A； PDBConstruct 130–267； UniProt 220–357 Author chain B； PDBConstruct 1–129； UniProt 1–129 Author chain B； PDBConstruct 130–267； UniProt 220–357 Author chain C； PDBConstruct 1–129； UniProt 1–129 Author chain C； PDBConstruct 130–267； UniProt 220–357 Author chain D； PDBConstruct 1–129； UniProt 1–129 Author chain D； PDBConstruct 130–267； UniProt 220–357

Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G

Streptococcus sp. group G

UniProt P06654

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 228–282 Chain B； UniProt 228–282 Chain C； UniProt 228–282 Chain D； UniProt 228–282	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 4.40 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9JA6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EM7 HELIX VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G Deposited 2000-03-16	Different construct Different mutation/modification 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 189–244（56 aa） Fragment：B1 DOMAIN	Mutation：A24E, K28R, Q32E, N35K, D36K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；100 mM sodium acetate, 30% polyethylene glycol momomethyl Ether 2000, 200 mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.267
1GB1 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G Deposited 1991-05-15	Different construct Different mutation/modification 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 228–282（55 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1IGC IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS Deposited 1994-08-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 293–352（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1IGD THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G: AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB Deposited 1994-08-05	Different construct Different mutation/modification 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 293–352（60 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.10 Å
1LE3 NMR Structure of Tryptophan Zipper 4: A Stable Beta-Hairpin Peptide Based on the C-terminal Hairpin of the B1 Domain of Protein G Deposited 2002-04-09	Different construct Different mutation/modification 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 267–282（16 aa） Fragment：C-terminal hairpin of the B1 domain of Protein G	Mutation：Y45W/F52W/V54W Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2mM trpzip4 \| 92% H2O, 8% D2O, pH 6.0, 0.1mM DSS	Resolution not provided
1MPE Ensemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain B 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain C 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain D 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282	Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.45；313 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate, 0.02% sodium azide；Pressure 1 NMR sample composition 3.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide \| 90% H2O/10% D2O NMR sample composition 2.89 mM (in monomer) U-15N, 50 mM sodium phosphate buffer, 0.02% sodium azide \| 90% H2O/10% D2O NMR sample composition 3.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide \| 100% D2O NMR sample composition 1.4 mM (in monomer) 1:1 mixture unlabelled:U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide \| 100% D2O	Resolution not provided
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain B 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain C 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain D 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282	Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.283
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain F 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain G 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain H 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282	Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.283
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain I 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain J 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain K 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282 Chain L 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282	Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.283
1PGA TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON WITH NMR Deposited 1993-11-23	Different construct Different mutation/modification 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 228–282（55 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.07 Å
1PGB TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR Deposited 1993-11-23	Different construct Different mutation/modification 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 228–282（55 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.92 Å
1PGX THE 1.66 ANGSTROMS X-RAY STRUCTURE OF THE B2 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON TO THE NMR STRUCTURE OF THE B1 DOMAIN Deposited 1992-04-03	Different construct Different mutation/modification 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 284–366（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.66 Å
1PN5 NMR structure of the NALP1 Pyrin domain (PYD) Deposited 2003-06-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 228–282（55 aa） Fragment：Pyrin domain (PYD)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Pressure 1 NMR sample composition 1mM NALP1 PYD U-15N,13C; 50mM Na / PO4 - Buffer; 50mM NaCl; 1mM CHAPS; 20mM DTT (D10); 0.02% NaN3; 0.1mM EDTA; protease inhibitor cocktail (Complete, Roche); 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
1Q10 Ensemble of 40 Structures of the Dimeric Mutant of the B1 Domain of Streptococcal Protein G Deposited 2003-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 228–282（55 aa） Fragment：B1 Domain Chain B 228–282（55 aa） Fragment：B1 Domain	Mutation：T228Q,L231V,F256V,Y259F,A260F Mutation：T228Q,L231V,F256V,Y259F,A260F	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate buffer；Pressure ambient NMR sample composition 1.7mM (in monomer) U-15N,13C, 50mM phosphate buffer, 0.02% NaN3, 92.5% H2O, 7.5% D2O \| 92.5% H2O, 7.5% D2O NMR sample composition 0.85mM (in monomer) U-15N,13C, 0.85mM (in monomer) unlabeled, 50mM phosphate buffer (pH 5.5), 0.02 % NaN3, 92.5% H2O, 7.5% D2O \| 92.5% H2O, 7.5% D2O NMR sample composition 0.85mM (in monomer) U-15N,13C, 0.85mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 100% D2O \| 100% D2O NMR sample composition 1.7mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 92.5% H2O, 7.5% D2O \| 92.5% H2O, 7.5% D2O NMR sample composition 1.7mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 100% D2O \| 100% D2O	Resolution not provided
2CWB Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin Deposited 2005-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 229–282（54 aa） Fragment：C-TERMINAL UBA DOMAIN,C-TERMINAL UBA DOMAIN	Mutation：I12A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient NMR sample composition 1mM HGB1-UBA U-15N,13C; 20mM phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2DEN Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin Deposited 2006-02-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 229–282（54 aa） Fragment：UBA domain,UBA domain	Mutation：I12A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 1mM HGB1-UBA \| 20mM phosphate, 100mM NaCl, pH6.5 NMR sample composition 1mM Ubiquitin \| 20mM phosphate, 100mM NaCl, pH6.5	Resolution not provided
2GB1 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G Deposited 1991-05-15	Different construct Different mutation/modification 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 228–282（55 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2IGD ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ANGSTROM RESOLUTION Deposited 1997-04-30	Different construct Different mutation/modification 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 293–352（60 aa） Fragment：IMMUNOGLOBULIN-BINDING DOMAIN III	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；CRYSTALS WERE GROWN BY HANGING DROP VAPOUR DIFFUSION FROM 24-26% PEG 4000, 10MM SODIUM ACETATE AT PH 4.8 AND 0.01% SODIUM AZIDE. CELL PARAMETERS ARE NOT THOSE DETERMINED EXPERIMENTALLY. THEY WERE ADJUSTED ON THE BASIS OF THE ENGH & HUBER DICTIONARY AT THE END OF REFINEMENT. THE EXPERIMENTAL ESTIMATES WERE KNOWN TO HAVE POTENTIAL ERRORS DUE TO INACCURACIES IN THE CRYSTAL-TO-DETECTOR AND WAVELENGTH CALIBRATION., vapor diffusion - hanging drop	Resolution 1.10 Å R-free 0.125
2IGH DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR Deposited 1992-08-26	Different construct Different mutation/modification 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 292–352（61 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2J52 Solution Structure of GB1 domain Protein G and low and high pressure. Deposited 2006-09-11	Different construct Different mutation/modification 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 228–282（55 aa） Fragment：RESIDUES 228-282	Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.4；287 K；Ionic strength (raw mmCIF value) 0.1；Pressure 30.0 NMR sample composition 90%WATER/10%D2O	Resolution not provided
2J53 Solution Structure of GB1 domain Protein G and low and high pressure. Deposited 2006-09-11	Different construct Different mutation/modification 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 228–282（55 aa） Fragment：RESIDUES 228-282	Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.4；287 K；Ionic strength (raw mmCIF value) 0.1；Pressure 2000.0 NMR sample composition 90%WATER/10%D2O	Resolution not provided
2JU6 Solid-State Protein Structure Determination with Proton-Detected Triple Resonance 3D Magic-Angle Spinning NMR Spectroscopy Deposited 2007-08-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 228–282（55 aa）	Mutation：T2Q	No recorded non-water small molecule	SOLID-STATE NMR NMR measurement conditions pH 5.5；281 K；Pressure ambient NMR sample composition 5 mM [U-13C; U-15N; U-2H] GB1, 50 % isopropyl alcohol, 25 % (4R)-2-Methylpentane-2,4-diol, 50 mM sodium phosphate, Solid Slurry \| Solid Slurry	Resolution not provided
2K0P Determination of a Protein Structure in the Solid State from NMR Chemical Shifts Deposited 2008-02-11	Different construct Different mutation/modification 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 228–282（55 aa） Fragment：GB1	Mutation：T2Q	No recorded non-water small molecule	SOLID-STATE NMR NMR measurement conditions 278 K；Pressure 1 NMR sample composition 10 mg/mL [U-100% 13C; U-100% 15N] GB1, 0.5 v/v Methyl Pentane diol, 0.25 v/v Isopropanol \| 0.5 v/v Methyl Pentane diol/0.25 v/v Isopropanol	Resolution not provided
2KBT Attachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method Deposited 2008-12-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 228–282（55 aa） Fragment：SH3 2 domain of Proto-oncogene vav,UNP residues 228-282 of Immunoglobulin G-binding protein G	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 20 mM MES-1, 2 mM DTT-2, 150 mM NaCl-3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LGI Atomic Resolution Protein Structures using NMR Chemical Shift Tensors Deposited 2011-07-26	Different construct Different mutation/modification 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 229–282（54 aa） Fragment：2-1 repeat region residues 229-282	Not recorded	No recorded non-water small molecule	SOLID-STATE NMR NMR measurement conditions pH 5.5；273 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 20 mg U-2-13C-glycerol; U-100% 15N GB1 \| solid	Resolution not provided
2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 229–282（54 aa） Fragment：UNP P06654 residues 229-282, UNP Q9UNA4 residues 516-555	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O \| 100% D2O NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O \| 100% D2O NMR sample composition 3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O \| 100% D2O	Resolution not provided
2N7J Sidechain chi1 distribution in B3 domain of protein G from extensive sets of residual dipolar couplings Deposited 2015-09-12	Different construct Different mutation/modification 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 299–352（54 aa） Fragment：residues 299-352	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K, 100% D2O \| 100% D2O NMR sample composition 1.3 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K, 100% D2O \| 100% D2O NMR sample composition 1.3 mM [U-13C; U-15N; U-2H] GB3-K19A/V42E/D47K, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E, 100% D2O \| 100% D2O NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E, 100% D2O \| 100% D2O NMR sample composition 2.0 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3, 100% D2O \| 100% D2O NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K, 100% D2O \| 100% D2O NMR sample composition 2.5 mM [U-13C; U-15N; U-2H] wild-type GB3, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6, 100% D2O \| 100% D2O NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E-CHis6, 100% D2O \| 100% D2O NMR sample composition 0.9 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E-CHis6, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2NMQ Simultaneous determination of protein structure and dynamics using rdcs Deposited 2006-10-23	Different construct Different mutation/modification 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 298–352（55 aa） Fragment：protein GB3(residues 298-352)	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2RMM Solution structure of GB1 A34F mutant Deposited 2007-10-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 229–282（54 aa） Chain B 229–282（54 aa）	Mutation：A34F Mutation：A34F	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 2.0mM [U-99% 13C; U-99% 15N] entity, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RPV Solution Structure of GB1 with LBT probe Deposited 2008-10-28	Different construct Different mutation/modification 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 227–282（56 aa） Fragment：L2GB	Mutation：E38C	LA LANTHANUM (III) ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.8mM [U-99% 13C; U-99% 15N] L2GB, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26	Different construct Different mutation/modification 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 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.20 Å R-free 0.181
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26	Different construct Different mutation/modification 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 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.20 Å R-free 0.181
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282) Chain B 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)	Not recorded	FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.20 Å R-free 0.181
6CNE Selenomethionine variant (V29SeM) of protein GB1 Deposited 2018-03-08	Different construct Different mutation/modification 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 229–282（54 aa）	Mutation：L5Sem Non-standard monomer：Yes (specific site not provided by mmCIF)	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；283.15 K；47% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 Non-reducing conditions (no TCEP)	Resolution 1.20 Å R-free 0.198
6CNE Selenomethionine variant (V29SeM) of protein GB1 Deposited 2018-03-08	Different construct Different mutation/modification 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 229–282（54 aa）	Mutation：L5Sem Non-standard monomer：Yes (specific site not provided by mmCIF)	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；283.15 K；47% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 Non-reducing conditions (no TCEP)	Resolution 1.20 Å R-free 0.198
6L91 X-ray structure of synthetic GB1 domain with the mutation K10(DVA). Deposited 2019-11-07	Different construct Different mutation/modification 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 227–282（56 aa）	Mutation：K10(DVA) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1M NaCacodylate (pH 5.5), 20% PEG 4000	Resolution 1.84 Å R-free 0.186
6L9B X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11A Deposited 2019-11-08	Different construct Different mutation/modification 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 227–282（56 aa）	Mutation：K10(DVA), T11A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.2M CaCl2, 0.1M sodium acetate (pH 4.6), 30% Isopropanol	Resolution 1.95 Å R-free 0.250
6L9D X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11S Deposited 2019-11-08	Different construct Different mutation/modification 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 227–282（56 aa）	Mutation：K10DVA, T11S Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Sodium Cacodylate (pH 6), 20% PEG 4000	Resolution 1.73 Å R-free 0.243
6LJI X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V Deposited 2019-12-16	Different construct Different mutation/modification 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 227–282（56 aa） Fragment：GB1 domain	Mutation：K10(DVA), T11V Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；20% PEG 4000, 0.1M MES pH 6.0	Resolution 1.84 Å R-free 0.328
6LJI X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V Deposited 2019-12-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 227–282（56 aa） Fragment：GB1 domain	Mutation：K10(DVA), T11V Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；20% PEG 4000, 0.1M MES pH 6.0	Resolution 1.84 Å R-free 0.328
6V9I cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) Deposited 2019-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 229–282（54 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20	Resolution 5.20 Å
7QTR GB1 in mammalian cells, 50 uM Deposited 2022-01-15	Different construct Different mutation/modification 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 229–282（54 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；283 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition 50 uM [U-13C; U-15N] B1 domain of streptococcal protein G (GB1), 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7QTS GB1 in mammalian cells, 10 uM Deposited 2022-01-15	Different construct Different mutation/modification 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 229–282（54 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；283 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition 10 uM [U-13C; U-15N] GB1, in-cell \| in-cell	Resolution not provided
7RXC CryoEM structure of KDELR with Legobody Deposited 2021-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 295–352（58 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7RXD CryoEM structure of RBD domain of COVID-19 in complex with Legobody Deposited 2021-08-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 295–352（58 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8JXR Structure of nanobody-bound DRD1_LSD complex Deposited 2023-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 295–352（58 aa）	Mutation：E360Q,K363A,D364F,T367I,R368L	7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
8JXS Structure of nanobody-bound DRD1_PF-6142 complex Deposited 2023-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 295–352（58 aa）	Mutation：E360Q,K363A,D364F,T367I,R368L,D404E,A405H	V6X 4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8T0G Backbone Dialkylation in Peptide Hairpins: Natural Backbone Prototype Deposited 2023-06-01	Different construct Different mutation/modification 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 267–282（16 aa）	Mutation：T13A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR sample composition 2 mM GB1 C-terminal Hairpin Mutant: Ala13 variant, 50 mM sodium phosphate, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9BDT Apolipoprotein B 100 bound to LDL receptor and legobody Deposited 2024-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 295–352（58 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.40 Å
9CHT Human E3 ligase E6AP in complex with HPV16-E6 and p53 Deposited 2024-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 228–282（55 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 295–352（58 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9G4T Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome Deposited 2024-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: monomeric	Chain A 229–282（54 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.51 Å
9JA5 Cryo-EM structure of Tdk1-Bdf1 complex Deposited 2024-08-24	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 228–282（55 aa） Chain B 228–282（55 aa） Chain C 228–282（55 aa） Chain D 228–282（55 aa） Chain E 228–282（55 aa） Chain F 228–282（55 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 2.70 Å
9W3K GPR151-Legobody complex Deposited 2025-07-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 295–352（58 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å

48 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPG1_STRSG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 278–332； UniProt 228–282 Author chain B； PDBConstruct 278–332； UniProt 228–282 Author chain C； PDBConstruct 278–332； UniProt 228–282 Author chain D； PDBConstruct 278–332； UniProt 228–282

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	9ja6
Deposition date deposition_date	2024-08-24
最后修订 last_revision	2024-11-13
Structure title title	Cryo-EM structure of Tdk1 tetramer complex
Keywords keywords	signaling protein, meiotic cell cycle, CELL CYCLE; CELL CYCLE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	33.79 Å
Radius of gyration Rg (electron density) rg_electron	33.95 Å
Forward intensity I(0) i0	85062900.00
Molecular weight molecular_weight	69534.0 kDa
Excluded volume excluded_volume	85693 Å³
Envelope volume envelope_volume	119010 Å³
Hydration-shell volume shell_volume	31886 Å³
Envelope diameter envelope_diameter	112.0 Å
Shell Rg shell_rg	36.91 Å
Envelope Rg envelope_rg	34.80 Å
Shape Rg shape_rg	33.96 Å
Total Rg total_rg	34.17 Å
Total atoms total_atoms	4880
Residues n_residues	588
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	108.0 Å
Rg (real space) rg_real	34.09 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	8.5060e+07
I(0) uncertainty (real space) i0_real_error	1.5180e+06
Rg (reciprocal space) rg_reciprocal	33.91 Å
I(0) (reciprocal space) i0_reciprocal	85050000.0000
Solution quality estimate total_estimate	0.7914
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.5 Å
Skewness Skewness skewness	0.569
Kurtosis Kurtosis kurtosis	-0.365
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11650000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.792; Smooth: 0.063

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	37724

Description description	Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G
Molecular weight formula_weight	38436.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4880

Cryo-EM structure of Tdk1 tetramer complex

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

Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G

State in the Current Structure

Other States of the Same Protein in the Database

Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Streptococcus sp. group G
NCBI Class编号 ncbi_taxonomy_id	1320
宿主生物 host_organism	Schizosaccharomyces pombe 972h-

fit	/app/data/saxs_computation/ja/9ja6/9ja6.fit
pddf	/app/data/pr_computation/ja/9ja6/9ja6.pr.out
profile	/app/data/saxs_computation/ja/9ja6/9ja6.dat