2wzp

Structures of Lactococcal Phage p2 Baseplate Shed Light on a Novel Mechanism of Host Attachment and Activation in Siphoviridae

Method: X-RAY DIFFRACTION

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

PUTATIVE RECEPTOR BINDING PROTEIN

LACTOCOCCUS PHAGE P2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 45	CAMELID VHH5 × 18 LACTOCOCCAL PHAGE P2 ORF15 × 6 LACTOCOCCAL PHAGE P2 ORF16 × 3 water × 42	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q1RNF7_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 2–264 Author chain B； PDBConstruct 1–263； UniProt 2–264 Author chain C； PDBConstruct 1–263； UniProt 2–264 Author chain G； PDBConstruct 1–263； UniProt 2–264 Author chain H； PDBConstruct 1–263； UniProt 2–264 Author chain I； PDBConstruct 1–263； UniProt 2–264

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	2wzp
Deposition date deposition_date	2009-12-01
Structure title title	Structures of Lactococcal Phage p2 Baseplate Shed Light on a Novel Mechanism of Host Attachment and Activation in Siphoviridae
Keywords keywords	BASEPLATE, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2wzp__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2wzp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wzp__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	76.28 Å
Rg (electron density)	75.46 Å
Total Rg	75.63 Å
Atom count	76914
Residues	9897
Excluded volume	1360600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wzp__assembly_1__model_1`	45-meric （45）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PUTATIVE RECEPTOR BINDING PROTEIN
Molecular weight formula_weight	28881.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,G,H,I
Atom count atom_count	27647

TIKNFTFFSPNSTEFPVGSNNDGKLYMMLTGMDYRTIRRKDWSSPLNTALNVQYTNTSIIAGGRYFELLNETVALKGDSVNYIHANIDLTQTANPVSLSAETANNSNGVDINNGSGVLKVCFDIVTTSGTGVTSTKPIVQTSTLDSISVNDMTVSGSIDVPVQTLTVEAGNGLQLQLTKKNNDLVIVRFFGSVSNIQKGWNMSGTWVDRPFRPAAVQSLVGHFAGRDTSFHIDINPNGSITWWGANIDKTPIATRGNGSYFIKSAW

Source Source

Source organism organism	LACTOCOCCUS PHAGE P2
NCBI taxonomy ID ncbi_taxonomy_id	254252
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	CAMELID VHH5
Molecular weight formula_weight	13499.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,J,K,L

QVQLQESGGGLVQAGGSLRLSCTASRRTGSNWCMGWFRQLAGKEPELVVALNFDYDMTYYADSVKGRFTVSRDSGKNTVYLQMNSLKPEDTAIYYCAARSGGFSSNRELYDGWGQGTQVTVSS

Source Source

Source organism organism	LAMA GLAMA
Common name common_name	LLAMA
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	LACTOCOCCAL PHAGE P2 ORF15
Molecular weight formula_weight	37899.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

MSYYHHHHHHLESTSLYKKAGLENLYFQGVRQYKIHTNLDGTDDKVWDVTNGKVRFYQPSNLGLQSTNNIWQSNGIGVMGTRSITQPQIEFKLETFGESLEENYQLMKDFVNDILSKKFVTLEYQTEIFQVYADLALADVTKTEGYGKNGTFSEKITFDIITKWYTYENLTFDKIQNGKVIAGMSKIYGGTAPGNYKYIKGTSYTYYGESDIDRLSRWDIKEEIFSFMGILYPKLPKTPAGVRFLDDIGNEYTAIVFKTEQVQDYILINTDVNDETYQGWKGTTALNLFPVMDFERYRTRIIEKGQMELINLSKAEFKIKRKADFV

Source Source

Source organism organism	LACTOCOCCUS PHAGE P2
NCBI taxonomy ID ncbi_taxonomy_id	254252
Host organism host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 polymer

Description description	LACTOCOCCAL PHAGE P2 ORF16
Molecular weight formula_weight	42883.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MLEANVYDNFNPNYYNISDFSMPNGKKEKRGLPIPKARCQVINYELWETGYLYTSSATLTVSVEVGDIVQILFPEVVPIEEALGKKKKLNLDMVYLVTDVDESNKATLKNYFWAMIESLDVPNAITKTTNFAIIDYLIDPNKNNLMSYGYFFNSSIFAGKATINRKAETSSAHDVAKRIFSKVQFQPTTTIQHAPSETDPRNLLFINFASRNWNRKRITTRVDIKQSVTMDTETIVERSAYNFAVVFVKNKATDDYTDPPKMYIAKNNGDVIDYSTYHGDGTDLPDVRTAKTLFYDRDDHGNPPELSTIKVEISPSTIVTRLIFNQNELLPLYVNDLVDIWYEGKLYSGYIADRVKTEFNDRLIFVESGDKPNVI

Source Source

Source organism organism	LACTOCOCCUS PHAGE P2
NCBI taxonomy ID ncbi_taxonomy_id	254252
Host organism host_organism	ESCHERICHIA COLI

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2009

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6. Fold Classification (SCOP + CATH) 41 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2wzpd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2wzpd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2wzpe1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2wzpe2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2wzpf1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2wzpf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2wzpj1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2wzpj2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2wzpk1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2wzpk2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2wzpl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2wzpl2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (29 domains)

Domain ID domain_id	2wzpA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	2wzpA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

Domain ID domain_id	2wzpB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	2wzpB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

Domain ID domain_id	2wzpC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	2wzpC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

Domain ID domain_id	2wzpD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2wzpE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2wzpF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2wzpG01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	2wzpG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

Domain ID domain_id	2wzpH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	2wzpH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

Domain ID domain_id	2wzpI01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	520 — Triple-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Phage fibre proteins

Domain ID domain_id	2wzpI02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1830 — Phage tail base-plate Siphoviridae RBP, head domain

Domain ID domain_id	2wzpJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2wzpK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2wzpL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2wzpP01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	2wzpP02
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	370 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2wzpP03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	880 —

Domain ID domain_id	2wzpP04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2wzpQ01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	2wzpQ02
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	370 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2wzpQ03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	880 —

Domain ID domain_id	2wzpQ04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2wzpR01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	300 — Phage tail proteins - horseshoe like beta roll fold
Homologous superfamily homologous superfamily	20 — Phage tail base-plate attachment protein, domain D1/D2

Domain ID domain_id	2wzpR02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	50 — Phage tail protein beta-alpha-beta fold
Homologous superfamily homologous superfamily	50 — Phage tail base-plate attachment protein, domain D4

Domain ID domain_id	2wzpR03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
Homologous superfamily homologous superfamily	20 — Phage tail base-plate attachment protein, domain D3

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Unit-cell length a length_a	202.881 Å
Unit-cell length b length_b	202.881 Å
Unit-cell length c length_c	760.520 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	108

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	38.070 Å
R factor r_factor	0.1794
R_work r_work	0.1789
R_free r_free	0.2078

Structures of Lactococcal Phage p2 Baseplate Shed Light on a Novel Mechanism of Host Attachment and Activation in Siphoviridae

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

PUTATIVE RECEPTOR BINDING PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2wzp__assembly_1__model_1

2wzp__assembly_1__model_1 | I(q)

2wzp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 41 domains

SCOP 2.08 (12 domains)

CATH v4.4 (29 domains)

7. Citations (2)

Structures of Lactococcal Phage p2 Baseplate Shed Light on a Novel Mechanism of Host Attachment and Activation in Siphoviridae

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

PUTATIVE RECEPTOR BINDING PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2wzp__assembly_1__model_1

2wzp__assembly_1__model_1 | I(q)

2wzp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 41 domains

SCOP 2.08 (12 domains)

CATH v4.4 (29 domains)

7. Citations (2)