4xr8

Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution

Method: X-RAY DIFFRACTION

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

Maltose-binding periplasmic protein, ubiquitin ligase E6AP

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Cellular tumor antigen p53 × 1 （P04637） Protein E6 × 1 （P03126） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 DI(HYDROXYETHYL)ETHER × 2 ZINC ION × 3 1,2-ETHANEDIOL × 1 water × 3	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 1	Cellular tumor antigen p53 × 1 （P04637） Protein E6 × 1 （P03126） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 DI(HYDROXYETHYL)ETHER × 2 ZINC ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–368； UniProt 27–393 Author chain B； PDBConstruct 2–368； UniProt 27–393

Cellular tumor antigen p53

Homo sapiens

UniProt P04637

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Maltose-binding periplasmic protein, ubiquitin ligase E6AP × 1 （P0AEX9） Protein E6 × 1 （P03126） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 DI(HYDROXYETHYL)ETHER × 2 ZINC ION × 3 1,2-ETHANEDIOL × 1 water × 3	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 1	Maltose-binding periplasmic protein, ubiquitin ligase E6AP × 1 （P0AEX9） Protein E6 × 1 （P03126） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 DI(HYDROXYETHYL)ETHER × 2 ZINC ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P53_HUMAN
Isoform	P04637-6
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–199； UniProt 55–253 Author chain D； PDBConstruct 1–199； UniProt 55–253

Protein E6

Human papillomavirus type 16

UniProt P03126

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Maltose-binding periplasmic protein, ubiquitin ligase E6AP × 1 （P0AEX9） Cellular tumor antigen p53 × 1 （P04637） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 DI(HYDROXYETHYL)ETHER × 2 ZINC ION × 3 1,2-ETHANEDIOL × 1 water × 3	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 1	Maltose-binding periplasmic protein, ubiquitin ligase E6AP × 1 （P0AEX9） Cellular tumor antigen p53 × 1 （P04637） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 DI(HYDROXYETHYL)ETHER × 2 ZINC ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VE6_HPV16
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–151； UniProt 8–158 Author chain H； PDBConstruct 1–151； UniProt 8–158

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	4xr8
Deposition date deposition_date	2015-01-20
Structure title title	Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution
Keywords keywords	;Human papillomavirus 16, E6 oncoprotein, Ubiquitin-Ligase E6AP, tumor suppressor p53, p53 degradation, viral protein-antitumor protein, VIRAL PROTEIN- ANTITUMOR PROTEIN complex ;; VIRAL PROTEIN/ ANTITUMOR 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.

4xr8__assembly_1__model_1

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

Download this curve (.dat)

4xr8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4xr8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.13 Å
Rg (electron density)	29.37 Å
Total Rg	30.19 Å
Atom count	5764
Residues	725
Excluded volume	102530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4xr8__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4xr8__assembly_2__model_1`	trimeric （3）	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 (8)

Entity 1 Entity 1 polymer

Description description	Maltose-binding periplasmic protein, ubiquitin ligase E6AP
Molecular weight formula_weight	41803.3 kDa
Mutation mutation	D83A,K84A,K240A,E360A,D364A,K363A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	12034

MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAELTLQELLGEER

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Cellular tumor antigen p53
Molecular weight formula_weight	22448.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 polymer

Description description	Protein E6
Molecular weight formula_weight	18301.1 kDa
Mutation mutation	C80S,C97S,C111S,C140S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H

MFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLDKKQRFHNIRGRWTGRCMSCSRSSRTRRETQL

Source Source

Source organism organism	Human papillomavirus type 16
NCBI taxonomy ID ncbi_taxonomy_id	333760
Host organism host_organism	Escherichia coli K-12

Entity 4 Entity 4 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	354

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4xr8c_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.2 — p53 DNA-binding domain-like

Domain ID domain_id	d4xr8d_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.2 — p53 DNA-binding domain-like

CATH v4.4 (6 domains)

Domain ID domain_id	4xr8C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

Domain ID domain_id	4xr8D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

Domain ID domain_id	4xr8F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	240 — CRO Repressor
Homologous superfamily homologous superfamily	40 — E6 early regulatory protein

Domain ID domain_id	4xr8F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	240 — CRO Repressor
Homologous superfamily homologous superfamily	40 — E6 early regulatory protein

Domain ID domain_id	4xr8H01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	240 — CRO Repressor
Homologous superfamily homologous superfamily	40 — E6 early regulatory protein

Domain ID domain_id	4xr8H02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	240 — CRO Repressor
Homologous superfamily homologous superfamily	40 — E6 early regulatory protein

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Unit-cell length a length_a	77.842 Å
Unit-cell length b length_b	128.939 Å
Unit-cell length c length_c	81.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	49.635 Å
R factor r_factor	0.1962
R_work r_work	0.1936
R_free r_free	0.2463

Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution

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

Maltose-binding periplasmic protein, ubiquitin ligase E6AP

State in the Current Structure

Other States of the Same Protein in the Database

Cellular tumor antigen p53

State in the Current Structure

Other States of the Same Protein in the Database

Protein E6

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

4xr8__assembly_1__model_1

4xr8__assembly_1__model_1 | I(q)

4xr8__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 (8)

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 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution

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

Maltose-binding periplasmic protein, ubiquitin ligase E6AP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cellular tumor antigen p53

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein E6

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

4xr8__assembly_1__model_1

4xr8__assembly_1__model_1 | I(q)

4xr8__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 (8)

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 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)