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7vii

cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom

Method: ELECTRON MICROSCOPY Dmax: 233.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Major capsid protein

Escherichia phage lambda

UniProt P03713

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 × 840 PDB declaration: 840-meric（840） 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 × 420 （P03712） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen NITROGEN Resolution 5.60 Å
2 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 5.60 Å
3 Protein heterocomplex Heteromer Protein × 70 PDB declaration: 70-meric（70） 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 × 35 （P03712） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen NITROGEN Resolution 5.60 Å
4 Protein heterocomplex Heteromer Protein × 84 PDB declaration: 84-meric（84） 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 × 42 （P03712） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen NITROGEN Resolution 5.60 Å
5 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 5.60 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 7VII 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
7VIK Asymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom Deposited 2021-09-27 Different structure-quality metrics Assembly 1 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 3.76 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 11 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 × 840 PDB declaration: 840-meric（840） 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 × 420 （P03713） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen NITROGEN Resolution 5.60 Å
2 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 5.60 Å
3 Protein heterocomplex Heteromer Protein × 70 PDB declaration: 70-meric（70） 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 × 35 （P03713） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen NITROGEN Resolution 5.60 Å
4 Protein heterocomplex Heteromer Protein × 84 PDB declaration: 84-meric（84） 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 × 42 （P03713） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen NITROGEN Resolution 5.60 Å
5 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 5.60 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 7VII 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
7VIK Asymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom Deposited 2021-09-27 Different structure-quality metrics Assembly 1 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 3.76 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 10 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.

SAXS scattering curve SAXS Profile

SAXS profile for 7vii

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7vii
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7vii
Deposition date deposition_date2021-09-27
Structure title titlecryoEM structure of bacteriophage lambda capsid at 5.6 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 methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier64.94 Å
Radius of gyration Rg (electron density) rg_electron65.06 Å
Forward intensity I(0) i01715750000.00
Molecular weight molecular_weight345710.0 kDa
Excluded volume excluded_volume431300 ų
Envelope volume envelope_volume666560 ų
Hydration-shell volume shell_volume86630 ų
Envelope diameter envelope_diameter225.0 Å
Shell Rg shell_rg60.88 Å
Envelope Rg envelope_rg65.52 Å
Shape Rg shape_rg65.05 Å
Total Rg total_rg65.03 Å
Total atoms total_atoms24325
Residues n_residues3136
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax233.5 Å
Rg (real space) rg_real65.17 Å
Rg uncertainty (real space) rg_real_error2.73 Å
I(0) (real space) i0_real1.7160e+09
I(0) uncertainty (real space) i0_real_error3.8070e+07
Rg (reciprocal space) rg_reciprocal64.69 Å
I(0) (reciprocal space) i0_reciprocal1714000000.0000
Solution quality estimate total_estimate0.8749
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary77.8 Å
Skewness Skewness skewness0.296
Kurtosis Kurtosis kurtosis-0.544
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0010
Highest regularization parameter α highest_alpha63250000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.854
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)