8xpm

Mature virion portal of phage lambda with DNA

Method: ELECTRON MICROSCOPY

▼

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

Portal protein B

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 66 DNA 2	Tail tube protein × 30 （P03733） Tail tube terminator protein × 6 （P03732） Head completion protein × 12 （P68660） DNA (104-MER) × 1 DNA (92-MER) × 1 Head-tail connector protein FII × 6 （P03714）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PORTL_LAMBD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–533； UniProt 1–533 Author chain B1； PDBConstruct 1–533； UniProt 1–533 Author chain B2； PDBConstruct 1–533； UniProt 1–533 Author chain B3； PDBConstruct 1–533； UniProt 1–533 Author chain B4； PDBConstruct 1–533； UniProt 1–533 Author chain B5； PDBConstruct 1–533； UniProt 1–533 Author chain b； PDBConstruct 1–533； UniProt 1–533 Author chain b1； PDBConstruct 1–533； UniProt 1–533 Author chain b2； PDBConstruct 1–533； UniProt 1–533 Author chain b3； PDBConstruct 1–533； UniProt 1–533 Author chain b4； PDBConstruct 1–533； UniProt 1–533 Author chain b5； PDBConstruct 1–533； UniProt 1–533

Tail tube protein

OrganismNot specified

UniProt P03733

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 66 DNA 2	Portal protein B × 12 （P03710） Tail tube terminator protein × 6 （P03732） Head completion protein × 12 （P68660） DNA (104-MER) × 1 DNA (92-MER) × 1 Head-tail connector protein FII × 6 （P03714）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TUBE_LAMBD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain O； PDBConstruct 1–246； UniProt 1–246 Author chain O1； PDBConstruct 1–246； UniProt 1–246 Author chain O2； PDBConstruct 1–246； UniProt 1–246 Author chain P； PDBConstruct 1–246； UniProt 1–246 Author chain P1； PDBConstruct 1–246； UniProt 1–246 Author chain P2； PDBConstruct 1–246； UniProt 1–246 Author chain Q； PDBConstruct 1–246； UniProt 1–246 Author chain Q1； PDBConstruct 1–246； UniProt 1–246 Author chain Q2； PDBConstruct 1–246； UniProt 1–246 Author chain R； PDBConstruct 1–246； UniProt 1–246 Author chain R1； PDBConstruct 1–246； UniProt 1–246 Author chain R2； PDBConstruct 1–246； UniProt 1–246 Author chain V； PDBConstruct 1–246； UniProt 1–246 Author chain V1； PDBConstruct 1–246； UniProt 1–246 Author chain V2； PDBConstruct 1–246； UniProt 1–246 Author chain o； PDBConstruct 1–246； UniProt 1–246 Author chain o1； PDBConstruct 1–246； UniProt 1–246 Author chain o2； PDBConstruct 1–246； UniProt 1–246 Author chain p； PDBConstruct 1–246； UniProt 1–246 Author chain p1； PDBConstruct 1–246； UniProt 1–246 Author chain p2； PDBConstruct 1–246； UniProt 1–246 Author chain q； PDBConstruct 1–246； UniProt 1–246 Author chain q1； PDBConstruct 1–246； UniProt 1–246 Author chain q2； PDBConstruct 1–246； UniProt 1–246 Author chain r； PDBConstruct 1–246； UniProt 1–246 Author chain r1； PDBConstruct 1–246； UniProt 1–246 Author chain r2； PDBConstruct 1–246； UniProt 1–246 Author chain v； PDBConstruct 1–246； UniProt 1–246 Author chain v1； PDBConstruct 1–246； UniProt 1–246 Author chain v2； PDBConstruct 1–246； UniProt 1–246

Tail tube terminator protein

OrganismNot specified

UniProt P03732

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 66 DNA 2	Portal protein B × 12 （P03710） Tail tube protein × 30 （P03733） Head completion protein × 12 （P68660） DNA (104-MER) × 1 DNA (92-MER) × 1 Head-tail connector protein FII × 6 （P03714）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TTTP_LAMBD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain U； PDBConstruct 1–131； UniProt 1–131 Author chain U1； PDBConstruct 1–131； UniProt 1–131 Author chain U2； PDBConstruct 1–131； UniProt 1–131 Author chain U3； PDBConstruct 1–131； UniProt 1–131 Author chain U4； PDBConstruct 1–131； UniProt 1–131 Author chain U5； PDBConstruct 1–131； UniProt 1–131

Head completion protein

OrganismNot specified

UniProt P68660

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 66 DNA 2	Portal protein B × 12 （P03710） Tail tube protein × 30 （P03733） Tail tube terminator protein × 6 （P03732） DNA (104-MER) × 1 DNA (92-MER) × 1 Head-tail connector protein FII × 6 （P03714）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HCP_LAMBD
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain W； PDBConstruct 1–68； UniProt 1–68 Author chain W1； PDBConstruct 1–68； UniProt 1–68 Author chain W2； PDBConstruct 1–68； UniProt 1–68 Author chain W3； PDBConstruct 1–68； UniProt 1–68 Author chain W4； PDBConstruct 1–68； UniProt 1–68 Author chain W5； PDBConstruct 1–68； UniProt 1–68 Author chain w； PDBConstruct 1–68； UniProt 1–68 Author chain w1； PDBConstruct 1–68； UniProt 1–68 Author chain w2； PDBConstruct 1–68； UniProt 1–68 Author chain w3； PDBConstruct 1–68； UniProt 1–68 Author chain w4； PDBConstruct 1–68； UniProt 1–68 Author chain w5； PDBConstruct 1–68； UniProt 1–68

Head-tail connector protein FII

OrganismNot specified

UniProt P03714

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 66 DNA 2	Portal protein B × 12 （P03710） Tail tube protein × 30 （P03733） Tail tube terminator protein × 6 （P03732） Head completion protein × 12 （P68660） DNA (104-MER) × 1 DNA (92-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FII_LAMBD
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain f； PDBConstruct 1–117； UniProt 1–117 Author chain f1； PDBConstruct 1–117； UniProt 1–117 Author chain f2； PDBConstruct 1–117； UniProt 1–117 Author chain f3； PDBConstruct 1–117； UniProt 1–117 Author chain f4； PDBConstruct 1–117； UniProt 1–117 Author chain f5； PDBConstruct 1–117； UniProt 1–117

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8xpm
Deposition date deposition_date	2024-01-04
Structure title title	Mature virion portal of phage lambda with DNA
Keywords keywords	;Bacteriophage, caudovirales, siphoviridae, portal vertex, portal, capsid, connector/neck, tail, delivery device, B-DNA, VIRAL PROTEIN-DNA COMPLEX ;; VIRAL PROTEIN/DNA
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8xpm__assembly_1__model_1

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

Download this curve (.dat)

8xpm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8xpm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	131.60 Å
Total Rg	131.10 Å
Atom count	120109
Residues	15448
Excluded volume	2101700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8xpm__assembly_1__model_1`	68-meric （68）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Portal protein B
Molecular weight formula_weight	59529.6 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,b,B1,b1,B2,b2,B3,b3,B4,b4,B5,b5
Atom count atom_count	120109

MKTPTIPTLLGPDGMTSLREYAGYHGGGSGFGGQLRSWNPPSESVDAALLPNFTRGNARADDLVRNNGYAANAIQLHQDHIVGSFFRLSHRPSWRYLGIGEEEARAFSREVEAAWKEFAEDDCCCIDVERKRTFTMMIREGVAMHAFNGELFVQATWDTSSSRLFRTQFRMVSPKRISNPNNTGDSRNCRAGVQINDSGAALGYYVSEDGYPGWMPQKWTWIPRELPGGRASFIHVFEPVEDGQTRGANVFYSVMEQMKMLDTLQNTQLQSAIVKAMYAATIESELDTQSAMDFILGANSQEQRERLTGWIGEIAAYYAAAPVRLGGAKVPHLMPGDSLNLQTAQDTDNGYSVFEQSLLRYIAAGLGVSYEQLSRNYAQMSYSTARASANESWAYFMGRRKFVASRQASQMFLCWLEEAIVRRVVTLPSKARFSFQEARSAWGNCDWIGSGRMAIDGLKEVQEAVMLIEAGLSTYEKECAKRGDDYQEIFAQQVRETMERRAAGLKPPAWAAAAFESGLRQSTEEEKSDSRAA

Entity 2 Entity 2 polymer

Description description	Tail tube protein
Molecular weight formula_weight	25831.8 kDa
Source method src_method	nat
Copy count entity_count	30

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,Q,R,V,v,V1,v1,V2,v2,o,O1,o1,O2,o2,p,P1,p1,P2,p2,q,Q1,q1,Q2,q2,r,R1,r1,R2,r2

MPVPNPTMPVKGAGTTLWVYKGSGDPYANPLSDVDWSRLAKVKDLTPGELTAESYDDSYLDDEDADWTATGQGQKSAGDTSFTLAWMPGEQGQQALLAWFNEGDTRAYKIRFPNGTVDVFRGWVSSIGKAVTAKEVITRTVKVTNVGRPSMAEDRSTVTAATGMTVTPASTSVVKGQSTTLTVAFQPEGVTDKSFRAVSADKTKATVSVSGMTITVNGVAAGKVNIPVVSGNGEFAAVAEITVTAS

Entity 3 Entity 3 polymer

Description description	Tail tube terminator protein
Molecular weight formula_weight	14659.1 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,U1,U2,U3,U4,U5

MKHTELRAAVLDALEKHDTGATFFDGRPAVFDEADFPAVAVYLTGAEYTGEELDSDTWQAELHIEVFLPAQVPDSELDAWMESRIYPVMSDIPALSDLITSMVASGYDYRRDDDAGLWSSADLTYVITYEM

Entity 4 Entity 4 polymer

Description description	Head completion protein
Molecular weight formula_weight	7625.7 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W,w,W1,w1,W2,w2,W3,w3,W4,w4,W5,w5

MTRQEELAAARAALHDLMTGKRVATVQKDGRRVEFTATSVSDLKKYIAELEVQTGMTQRRRGPAGFYV

Entity 5 Entity 5 polymer

Description description	DNA (104-MER)
Molecular weight formula_weight	32011.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	DA

CTGCACCAAACTACCGGAGGTGCGTGCAACACTATACATCTACTATTAGTAATAGTGAAATGCCCAGGAAAGGCCACTAGGCTGTCCAATGCCCCGCCGCTGGA

Entity 6 Entity 6 polymer

Description description	DNA (92-MER)
Molecular weight formula_weight	28412.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	DB

GCATTGGACAGCCTAGTGGCCTTTCCTGGGCATTTCACTATTACTAATAGTAGATGTATAGTGTTGCACGCACCTCCGGTAGTTTGGTGCAG

Entity 7 Entity 7 polymer

Description description	Head-tail connector protein FII
Molecular weight formula_weight	12775.0 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f,f1,f2,f3,f4,f5

MADFDNLFDAAIARADETIRGYMGTSATITSGEQSGAVIRGVFDDPENISYAGQGVRVEGSSPSLFVRTDEVRQLRRGDTLTIGEENFWVDRVSPDDGGSCHLWLGRGVPPAVNRRR

▶

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	triclinic

Resolution resolution	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	19060

Mature virion portal of phage lambda with DNA

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

Portal protein B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tail tube 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

Tail tube terminator 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

Head completion 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

Head-tail connector protein FII

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

8xpm__assembly_1__model_1

8xpm__assembly_1__model_1 | I(q)

8xpm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

7. Citations (1)