9MKB | pdb_00009mkb

Structure of the bacteriophage T4 portal-neck-tail complex

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
CK [auth S0]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
CK [auth S0]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
DK [auth S1]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
DK [auth S1]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
EK [auth S2]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
EK [auth S2]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
FK [auth S3]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
FK [auth S3]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
HK [auth S5]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
HK [auth S5]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
KK [auth S8]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
KK [auth S8]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
MK [auth SO]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
MK [auth SO]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
OK [auth SQ]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
OK [auth SQ]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
RK [auth Sx]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
RK [auth Sx]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
TK [auth Sz]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
TK [auth Sz]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
SK [auth Sy]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
SK [auth Sy]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
QK [auth Sw]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
QK [auth Sw]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
PK [auth Sv]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
PK [auth Sv]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
NK [auth SP]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
NK [auth SP]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
LK [auth SA]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
LK [auth SA]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
JK [auth S7]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
JK [auth S7]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
IK [auth S6]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)
IK [auth S6]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
GK [auth S4]SCOP2B SuperfamilyPhage fibre proteins 8044403 3000351 SCOP2B (2022-06-29)
GK [auth S4]SCOP2B SuperfamilyReceptor-binding domain of short tail fibre protein gp12 8033955 3001249 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF07068Major capsid protein Gp23 (Gp23)Major capsid protein Gp23- Family
PF07068Major capsid protein Gp23 (Gp23)Major capsid protein Gp23- Family
PF07068Major capsid protein Gp23 (Gp23)Major capsid protein Gp23- Family
PF07068Major capsid protein Gp23 (Gp23)Major capsid protein Gp23- Family
PF07068Major capsid protein Gp23 (Gp23)Major capsid protein Gp23- Family
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		PF07068Major capsid protein Gp23 (Gp23)Major capsid protein Gp23- Family
PF07484Phage Tail Collar Domain (Collar)Phage Tail Collar DomainThis region is occasionally found in conjunction with Pfam:PF03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in ...This region is occasionally found in conjunction with Pfam:PF03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions ([1]). A related protein Swiss:Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (Swiss:P10930) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop ([2]) and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of Swiss:P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution.
Domain
PF14928Short tail fibre protein receptor-binding domain (S_tail_recep_bd)Short tail fibre protein receptor-binding domainThis domain is a receptor binding domain found on bacteriophage short tail fibre proteins. It contains a zinc-binding site and a potential lipopolysaccharide-binding site [1]. Domain
PF09089Phage short tail fibre protein gp12, middle domain (gp12-short_mid)Phage short tail fibre protein gp12, middle domain- Repeat
PF22670Baseplate wedge protein gp10 domain 3 (Gp10_D3)Baseplate wedge protein gp10 domain 3This domain is found in Baseplate wedge protein gp10 and related proteins. This domain folds into a beta-sandwich. Domain
PF07880Bacteriophage T4 gp9/10-like protein, N-terminal (T4_gp9_10_N)Bacteriophage T4 gp9/10-like protein, N-terminalThis entry represents the N-terminal domain of Baseplate protein gp9 from Bacteriophage T4, a component of the viral baseplate [1]. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment t ...This entry represents the N-terminal domain of Baseplate protein gp9 from Bacteriophage T4, a component of the viral baseplate [1]. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment to a host cell. The protein is active as a trimer, with each monomer being composed of three domains. The N-terminal domain consists of an extended polypeptide chain and two alpha helices. The alpha1 helix from each of the three monomers in the trimer interacts with its counterparts to form a coiled-coil structure. The middle domain is a seven-stranded beta-sandwich. This entry represents the region including these two domains. Noticeably, the long flexible region between N-terminal and middle domains may be required for the function of gp9 to transmit signals from the long tail fibres [2]. Together with gp11, gp10 initiates the assembly of wedges that then go on to associate with a hub to form the viral baseplate [1].
Domain
PF21939Baseplate structural protein Gp10, C-terminal domain (Gp10_C)Baseplate structural protein Gp10, C-terminal domainThis entry represents the C-terminal domain (CTD) of baseplate structural protein Gp10 that assembles into trimeric structures. The core structure and assembly of Gp10 has structural similarity to that of the head domain of Gp11 and the receptor bind ...This entry represents the C-terminal domain (CTD) of baseplate structural protein Gp10 that assembles into trimeric structures. The core structure and assembly of Gp10 has structural similarity to that of the head domain of Gp11 and the receptor binding domain of Gp12 [1]. The monomeric CTD of Gp10 consists of an alpha-helix followed by a three-stranded, antiparallel beta-sheet, which is almost perpendicular to the helix. The three symmetry related beta-sheets interact with their first beta-strands in the trimer, thus creating a flower-like arrangement with the alpha-helices being the flower stem and the three beta-sheets being the petals.
Domain
PF23618Bacteriophage T4 gp9/10-like protein, C-terminal (T4_gp9_10_C)Bacteriophage T4 gp9/10-like protein, C-terminalThis entry represents the C-terminal domain of Baseplate protein gp9 from Bacteriophage T4, a component of the viral baseplate [1]. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment t ...This entry represents the C-terminal domain of Baseplate protein gp9 from Bacteriophage T4, a component of the viral baseplate [1]. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment to a host cell. The protein is active as a trimer, with each monomer being composed of three domains. The C-terminal domain is thought to be essential for trimerisation and is organised into an eight- stranded antiparallel beta-barrel, which was found to resemble the 'jelly roll' fold found in many viral capsid proteins [2]. Together with gp11, gp10 initiates the assembly of wedges that then go on to associate with a hub to form the viral baseplate [1].
Domain
PF21428Baseplate wedge protein gp7, helical domain (Gp7_helical)Baseplate wedge protein gp7, helical domainThis domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and inf ...This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents helix-turn-helix motif that is part of the long linker connecting the second and fourth domains [1].
Domain
PF21427Baseplate wedge protein gp7, domain V (Gp7_5th)Baseplate wedge protein gp7, domain VThis domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and inf ...This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents Domain V, which is an insertion into domain IV and consists of an eight-stranded beta- barrel followed by two short alpha-helices [1].
Domain
PF21456Baseplate wedge protein gp7, domain VI (Gp7_6th)Baseplate wedge protein gp7, domain VIThis domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and inf ...This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents Domain VI, which forms a ribbon-like structure that interacts with N-terminal region of the protein Gp10 [1].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
gp14, neck protein- -
gp18, tail sheath protein-
gp19, tail tube protein - -
gpwac, fibritin- -
gp23, major capsid protein- -
gp13, neck protein- -
gp15, tail terminator protein- - -
gp3, tube terminator protein - -
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		Hoc, highly immunogenic outer capsid protein- -
Soc, small outer capsid protein- -
gp12, short tail fiber protein
gp9, baseplate wedge tail fiber connector- -
gp11, baseplate wedge protein- - -
gp10, baseplate wedge protein-
gp8, baseplate wedge protein- - -
gp6, baseplate wedge protein
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		gp5, baseplate central spike protein
BQ [auth gd]gp5.4, tip of the central spike- - -
gp25, baseplate protein- - -
gp48, baseplate protein- - -
gp54, baseplate protein-
unassigned peptide A---
KT [auth uR],
LT [auth uV],
MT [auth uW]		unassigned peptide D---
OT [auth vZ],
PT [auth va],
QT [auth vb]		unassigned peptide E---
gp20, portal protein-
GT [auth tS],
HT [auth tX],
IT [auth tY]		unassigned peptide C---
CT [auth sQ],
DT [auth sT],
ET [auth sU]		unassigned peptide B---
gp53, baseplate wedge protein- - -
MR [auth ja],
NR [auth jb],
OR [auth jc]		gp29, tape measure protein-
IR [auth iC],
JR [auth iD],
KR [auth iF]		gp27, baseplate hub protein- -
gp7, baseplate wedge protein-

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR021674Bacteriophage T4, Gp14, neck proteinFamily
IPR052042Tail sheath structural proteinFamily
IPR054565Tail sheath protein Gp18-like, domain IDomain
IPR020287Tail sheath protein, C-terminal domainDomain
IPR054564Tail sheath protein Gp18-like, domain III N-terminal regionDomain
IPR035089Tail sheath protein, subtilisin-like domainDomain
IPR035326Phage tail sheath protein-like, beta-sandwich domainDomain
IPR010667Bacteriophage T4, Gp19, tail tubeFamily
IPR012473Fibritin C-terminalDomain
IPR010762Capsid protein, T4-like bacteriophage-likeFamily
IPR038997Major capsid protein, MyoviridaeFamily
IPR031997Myoviridae tail sheath stabiliserFamily
IPR038553Myoviridae tail sheath stabiliser superfamilyHomologous Superfamily
IPR010667Bacteriophage T4, Gp19, tail tubeFamily
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		IPR038998Highly immunogenic outer capsid proteinFamily
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		IPR035986PKD domain superfamilyHomologous Superfamily
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		IPR013783Immunoglobulin-like foldHomologous Superfamily
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		IPR022409PKD/Chitinase domainDomain
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		IPR000601PKD domainDomain
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
LA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]		IPR007110Immunoglobulin-like domainDomain
IPR038151Small outer capsid protein superfamilyHomologous Superfamily
IPR031743Small outer capsid proteinFamily
IPR037053Phage tail collar domain superfamilyHomologous Superfamily
IPR027448Short tail fibre protein, C-terminalDomain
IPR044916Short tail fibre protein, C-terminal superfamilyHomologous Superfamily
IPR015173Bacteriophage T4, Gp12Domain
IPR011083Phage tail collar domainDomain
IPR036240Gp9-like superfamilyHomologous Superfamily
IPR008987Baseplate structural protein Gp9/Gp10, N-terminal domainDomain
IPR027412Baseplate structural protein Gp9 C-terminal domain superfamilyHomologous Superfamily
IPR056391Baseplate protein gp9-like, C-terminalDomain
IPR027411Baseplate structural protein Gp9/Gp10 middle domain superfamilyHomologous Superfamily
IPR015982Baseplate structural protein Gp11, N-terminal domain superfamilyHomologous Superfamily
IPR015976Bacteriophage T4, Gp11, C-terminal finger domainHomologous Superfamily
IPR043180Baseplate structural protein Gp11, C-terminal domainHomologous Superfamily
IPR014791Baseplate structural protein Gp11Family
IPR036214Baseplate structural protein Gp11 superfamilyHomologous Superfamily
IPR036240Gp9-like superfamilyHomologous Superfamily
IPR008987Baseplate structural protein Gp9/Gp10, N-terminal domainDomain
IPR054430Baseplate wedge protein gp10, domain 3Domain
IPR056391Baseplate protein gp9-like, C-terminalDomain
IPR053827Baseplate structural protein Gp10, C-terminal domainDomain
IPR027411Baseplate structural protein Gp9/Gp10 middle domain superfamilyHomologous Superfamily
IPR034695Baseplate wedge protein gp10Family
IPR036327Bacteriophage T4, Gp8 superfamilyHomologous Superfamily
IPR015298Bacteriophage T4, Gp8Domain
IPR054065Baseplate wedge protein gp6, C-terminal domain IIIDomain
IPR034698Baseplate wedge protein gp6Family
IPR049027Baseplate structural protein gp6, C-terminal domain IDomain
IPR049026Baseplate wedge protein gp6-like, N-terminal helical domainDomain
IPR049028Baseplate structural protein gp6, C-terminal domain IIDomain
IPR049029Baseplate wedge protein gp6, domain II, firstDomain
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		IPR052619Bacteriophage lysozyme-likeFamily
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		IPR009590Protein Gp5, N-terminal OB-fold domainDomain
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		IPR023347Lysozyme domain superfamilyHomologous Superfamily
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		IPR023346Lysozyme-like domain superfamilyHomologous Superfamily
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		IPR046397Pre-baseplate central spike protein Gp5Family
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		IPR001165T4-type lysozymeFamily
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		IPR010609Gp5, C-terminalRepeat
AQ [auth gH],
YP [auth gE],
ZP [auth gG]		IPR002196Glycoside hydrolase, family 24Family
BQ [auth gd]IPR008727PAAR motifRepeat
IPR007048IraD/Gp25-likeDomain
IPR024389Baseplate tail-tube protein gp48, T4-like virusFamily
IPR010823Portal protein Gp20Family
IPR022607Baseplate wedge protein gp53, bacteriophage T4Family
MR [auth ja],
NR [auth jb],
OR [auth jc]		IPR057967Tape measure protein-likeFamily
IR [auth iC],
JR [auth iD],
KR [auth iF]		IPR015180Bacteriophage T4, Gp27, baseplate hub, C-terminalDomain
IR [auth iC],
JR [auth iD],
KR [auth iF]		IPR043084Gp27, baseplate hub, domain 4Homologous Superfamily
IR [auth iC],
JR [auth iD],
KR [auth iF]		IPR043083Gp27, baseplate hub, domain 3Homologous Superfamily
IR [auth iC],
JR [auth iD],
KR [auth iF]		IPR043085Gp27, baseplate hub, domain 2Homologous Superfamily
IR [auth iC],
JR [auth iD],
KR [auth iF]		IPR015181Bacteriophage T4, Gp27, baseplate hub, N-terminalDomain
IR [auth iC],
JR [auth iD],
KR [auth iF]		IPR043504Peptidase_S1_PA_chymotrypsinUnknown
IPR034697Baseplate wedge protein gp7Family
IPR048812Baseplate wedge protein gp7, domain VIDomain
IPR013783Immunoglobulin-like foldHomologous Superfamily
IPR048810Baseplate wedge protein gp7, helical domainDomain
IPR003961Fibronectin type IIIDomain
IPR048811Baseplate wedge protein gp7, domain VDomain
IPR036116Fibronectin type III superfamilyHomologous Superfamily