SAXSdb — 7vik

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

Major capsid protein

Escherichia phage lambda

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 × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain A； UniProt 1–341 Chain B； UniProt 1–341 Chain C； UniProt 1–341 Chain D； UniProt 1–341 Chain E； UniProt 1–341 Chain F； UniProt 1–341 Chain G； UniProt 1–341	Not recorded	Capsid decoration protein × 7 （P03712）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 3.76 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 7VIK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SJ5 Bacteriophage lambda major capsid protein mutant - W308A Deposited 2021-10-15	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 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa）	Mutation：W308A Mutation：W308A Mutation：W308A Mutation：W308A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291.15 K；0.1 M bis-tris, 0.1 M ammonium sulfate, 5% v/v glycerol, 30% v/v PEG-3350	Resolution 2.69 Å R-free 0.230
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 420 PDB declaration: 420-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different oligomeric state Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different oligomeric state Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different oligomeric state Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 42 PDB declaration: 42-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VI9 Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom Deposited 2021-09-26	Different oligomeric state Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.03 Å
7VIA Focused refinement of asymmetric unit of bacteriophage lambda procapsid at 3.88 Angstrom Deposited 2021-09-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.88 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 840 PDB declaration: 840-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different oligomeric state Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 70 PDB declaration: 70-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different oligomeric state Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
8K39 Structure of the bacteriophage lambda portal vertex Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain 0 1–341（341 aa） Chain 1 1–341（341 aa） Chain 2 1–341（341 aa） Chain 3 1–341（341 aa） Chain 4 1–341（341 aa） Chain 5 1–341（341 aa） Chain 6 1–341（341 aa） Chain 7 1–341（341 aa） Chain A 1–341（341 aa） Chain B 1–341（341 aa） Chain C 1–341（341 aa） Chain D 1–341（341 aa） Chain E 1–341（341 aa） Chain F 1–341（341 aa） Chain G 1–341（341 aa） Chain H 1–341（341 aa） Chain I 1–341（341 aa） Chain J 1–341（341 aa） Chain K 1–341（341 aa） Chain L 1–341（341 aa） Chain M 1–341（341 aa） Chain N 1–341（341 aa） Chain O 1–341（341 aa） Chain P 1–341（341 aa） Chain Q 1–341（341 aa） Chain R 1–341（341 aa） Chain S 1–341（341 aa） Chain T 1–341（341 aa） Chain g 1–341（341 aa） Chain h 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8XOU Prohead portal vertex of bacteriophage lambda Deposited 2024-01-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain A0 1–341（341 aa） Chain A1 1–341（341 aa） Chain A2 1–341（341 aa） Chain A3 1–341（341 aa） Chain A4 1–341（341 aa） Chain C0 1–341（341 aa） Chain C1 1–341（341 aa） Chain C2 1–341（341 aa） Chain C3 1–341（341 aa） Chain C4 1–341（341 aa） Chain D0 1–341（341 aa） Chain D1 1–341（341 aa） Chain D2 1–341（341 aa） Chain D3 1–341（341 aa） Chain D4 1–341（341 aa） Chain E0 1–341（341 aa） Chain E1 1–341（341 aa） Chain E2 1–341（341 aa） Chain E3 1–341（341 aa） Chain E4 1–341（341 aa） Chain F0 1–341（341 aa） Chain F1 1–341（341 aa） Chain F2 1–341（341 aa） Chain F3 1–341（341 aa） Chain F4 1–341（341 aa） Chain G0 1–341（341 aa） Chain G1 1–341（341 aa） Chain G2 1–341（341 aa） Chain G3 1–341（341 aa） Chain G4 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.58 Å
8XQB Mature virion portal vertex of bacteriophage lambda Deposited 2024-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 71 PDB declaration: 71-meric	Chain A0 1–341（341 aa） Chain A1 1–341（341 aa） Chain A2 1–341（341 aa） Chain A3 1–341（341 aa） Chain A4 1–341（341 aa） Chain C0 1–341（341 aa） Chain C1 1–341（341 aa） Chain C2 1–341（341 aa） Chain C3 1–341（341 aa） Chain C4 1–341（341 aa） Chain G0 1–341（341 aa） Chain G1 1–341（341 aa） Chain G2 1–341（341 aa） Chain G3 1–341（341 aa） Chain G4 1–341（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.07 Å

7 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CAPSD_LAMBD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–341； UniProt 1–341 Author chain B； PDBConstruct 1–341； UniProt 1–341 Author chain C； PDBConstruct 1–341； UniProt 1–341 Author chain D； PDBConstruct 1–341； UniProt 1–341 Author chain E； PDBConstruct 1–341； UniProt 1–341 Author chain F； PDBConstruct 1–341； UniProt 1–341 Author chain G； PDBConstruct 1–341； UniProt 1–341

Capsid decoration protein

Escherichia phage lambda

UniProt P03712

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 × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain H； UniProt 1–110 Chain I； UniProt 1–110 Chain J； UniProt 1–110 Chain K； UniProt 1–110 Chain L； UniProt 1–110 Chain M； UniProt 1–110 Chain N； UniProt 1–110	Not recorded	Major capsid protein × 7 （P03713）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 3.76 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 7VIK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C5E BACTERIOPHAGE LAMBDA HEAD PROTEIN D Deposited 1999-11-18	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 × 3 PDB declaration: trimeric	Chain A 16–110（95 aa） Chain B 16–110（95 aa） Chain C 16–110（95 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；28% PEG 4000, 0.1 M BIS-TRIS PH 6.5, 10 % GLYCEROL	Resolution 1.10 Å R-free 0.133
1TCZ Crystal structure of a truncated version of the phage lamda protein gpD Deposited 2004-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 16–110（95 aa） Fragment：N-terminal truncation Chain B 16–110（95 aa） Fragment：N-terminal truncation Chain C 16–110（95 aa） Fragment：N-terminal truncation	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；Tris-HCl, PEG 4000, Mg acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.232
1TCZ Crystal structure of a truncated version of the phage lamda protein gpD Deposited 2004-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 16–110（95 aa） Fragment：N-terminal truncation Chain E 16–110（95 aa） Fragment：N-terminal truncation Chain F 16–110（95 aa） Fragment：N-terminal truncation	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；Tris-HCl, PEG 4000, Mg acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.232
1VD0 Capsid stabilizing protein GPD, NMR, 20 Structures Deposited 2004-03-17	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 2–110（109 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Pressure AMBIENT NMR sample composition 1.3mm 15N labelled GPD, 20mm sodium phosphate \| 90% H2O/10% D2O NMR sample composition 1.3mm GPD, 50mm sodium phosphate \| 100% D2O	Resolution not provided
5MFD Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 Deposited 2016-11-18	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 × 2 PDB declaration: dimeric	Chain B 21–110（90 aa） Fragment：UNP residues 21-110	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
5MFD Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 Deposited 2016-11-18	Different construct Different mutation/modification 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 21–110（90 aa） Fragment：UNP residues 21-110	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
5MFD Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 Deposited 2016-11-18	Different construct Different mutation/modification 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 21–110（90 aa） Fragment：UNP residues 21-110	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
5MFD Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 Deposited 2016-11-18	Different construct Different mutation/modification 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 21–110（90 aa） Fragment：UNP residues 21-110	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 840 PDB declaration: 840-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different oligomeric state Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 70 PDB declaration: 70-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different oligomeric state Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
8XQB Mature virion portal vertex of bacteriophage lambda Deposited 2024-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 71 PDB declaration: 71-meric	Chain H0 1–110（110 aa） Chain H1 1–110（110 aa） Chain H2 1–110（110 aa） Chain H3 1–110（110 aa） Chain H4 1–110（110 aa） Chain I0 1–110（110 aa） Chain I1 1–110（110 aa） Chain I2 1–110（110 aa） Chain I3 1–110（110 aa） Chain I4 1–110（110 aa） Chain J0 1–110（110 aa） Chain J1 1–110（110 aa） Chain J2 1–110（110 aa） Chain J3 1–110（110 aa） Chain J4 1–110（110 aa） Chain N0 1–110（110 aa） Chain N1 1–110（110 aa） Chain N2 1–110（110 aa） Chain N3 1–110（110 aa） Chain N4 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.07 Å

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

View Construct and Data Evidence

UniProt name	DECO_LAMBD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–110； UniProt 1–110 Author chain I； PDBConstruct 1–110； UniProt 1–110 Author chain J； PDBConstruct 1–110； UniProt 1–110 Author chain K； PDBConstruct 1–110； UniProt 1–110 Author chain L； PDBConstruct 1–110； UniProt 1–110 Author chain M； PDBConstruct 1–110； UniProt 1–110 Author chain N； PDBConstruct 1–110； UniProt 1–110

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7vik
Deposition date deposition_date	2021-09-27
Structure title title	Asymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom
Keywords keywords	;bacteriophage lambda; capsid; procapsid; capsid maturation; virus structure; cryo-EM; auxiliary protein; conformational expansion; cementing protein; DNA packaging, VIRUS ;; VIRUS
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	64.96 Å
Radius of gyration Rg (electron density) rg_electron	65.08 Å
Forward intensity I(0) i0	1716980000.00
Molecular weight molecular_weight	345710.0 kDa
Excluded volume excluded_volume	431300 Å³
Envelope volume envelope_volume	665840 Å³
Hydration-shell volume shell_volume	87154 Å³
Envelope diameter envelope_diameter	227.6 Å
Shell Rg shell_rg	60.51 Å
Envelope Rg envelope_rg	65.22 Å
Shape Rg shape_rg	65.07 Å
Total Rg total_rg	65.04 Å
Total atoms total_atoms	24325
Residues n_residues	3136
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	232.0 Å
Rg (real space) rg_real	65.17 Å
Rg uncertainty (real space) rg_real_error	3.22 Å
I(0) (real space) i0_real	1.7170e+09
I(0) uncertainty (real space) i0_real_error	4.0330e+07
Rg (reciprocal space) rg_reciprocal	64.71 Å
I(0) (reciprocal space) i0_reciprocal	1715000000.0000
Solution quality estimate total_estimate	0.8751
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	77.3 Å
Skewness Skewness skewness	0.295
Kurtosis Kurtosis kurtosis	-0.549
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	64130000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.835

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Major capsid protein
Molecular weight formula_weight	38229.2 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	24346

MSMYTTAQLLAANEQKFKFDPLFLRLFFRESYPFTTEKVYLSQIPGLVNMALYVSPIVSGEVIRSRGGSTSEFTPGYVKPKHEVNPQMTLRRLPDEDPQNLADPAYRRRRIIMQNMRDEELAIAQVEEMQAVSAVLKGKYTMTGEAFDPVEVDMGRSEENNITQSGGTEWSKRDKSTYDPTDDIEAYALNASGVVNIIVFDPKGWALFRSFKAVKEKLDTRRGSNSELETAVKDLGKAVSYKGMYGDVAIVVYSGQYVENGVKKNFLPDNTMVLGNTQARGLRTYGCIQDADAQREGINASARYPKNWVTTGDPAREFTMIQSAPLMLLADPDEFVSVQLA

来源 Source

来源生物 organism	Escherichia phage lambda
通用名 common_name	Bacteriophage lambda
NCBI Class编号 ncbi_taxonomy_id	10710
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Capsid decoration protein
Molecular weight formula_weight	11582.9 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I,J,K,L,M,N

MTSKETFTHYQPQGNSDPAHTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIV

来源 Source

来源生物 organism	Escherichia phage lambda
通用名 common_name	Bacteriophage lambda
NCBI Class编号 ncbi_taxonomy_id	10710
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	7vikH01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	7vikI01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	7vikJ01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	7vikK01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	7vikL01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	7vikM01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

Domain ID domain_id	7vikN01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

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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	3.76 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	835912

fit	/app/data/saxs_computation/vi/7vik/7vik.fit
pddf	/app/data/pr_computation/vi/7vik/7vik.pr.out
profile	/app/data/saxs_computation/vi/7vik/7vik.dat

Asymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom

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

Major capsid protein

State in the Current Structure

Other States of the Same Protein in the Database

Capsid decoration protein

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)