SAXSdb — 6owt

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

AP-2 complex subunit alpha

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	AP-2 complex subunit beta × 1 （P62944） Adaptor protein complex AP-2, mu1 × 1 （Q5FWI9） Tetherin,Protein Nef × 2 （C3VHQ5,Q4JGV0） AP-2 complex subunit sigma × 1 （P62744）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q66HM2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–939； UniProt 1–939

AP-2 complex subunit beta

Rattus norvegicus

UniProt P62944

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） Adaptor protein complex AP-2, mu1 × 1 （Q5FWI9） Tetherin,Protein Nef × 2 （C3VHQ5,Q4JGV0） AP-2 complex subunit sigma × 1 （P62744）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2B1_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–591； UniProt 1–591

Adaptor protein complex AP-2, mu1

Mus musculus

UniProt Q5FWI9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） AP-2 complex subunit beta × 1 （P62944） Tetherin,Protein Nef × 2 （C3VHQ5,Q4JGV0） AP-2 complex subunit sigma × 1 （P62744）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5FWI9_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–141； UniProt 1–141

Tetherin,Protein Nef

Simian immunodeficiency virus

UniProt C3VHQ5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） AP-2 complex subunit beta × 1 （P62944） Adaptor protein complex AP-2, mu1 × 1 （Q5FWI9） AP-2 complex subunit sigma × 1 （P62744）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3VHQ5_CERAT
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain N； PDBConstruct 1–21； UniProt 4–24 Author chain T； PDBConstruct 1–21； UniProt 4–24

Tetherin,Protein Nef

Simian immunodeficiency virus

UniProt Q4JGV0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） AP-2 complex subunit beta × 1 （P62944） Adaptor protein complex AP-2, mu1 × 1 （Q5FWI9） AP-2 complex subunit sigma × 1 （P62744）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4JGV0_SIV
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain N； PDBConstruct 34–275； UniProt 1–251 Author chain T； PDBConstruct 34–275； UniProt 1–251

AP-2 complex subunit sigma

Rattus norvegicus

UniProt P62744

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） AP-2 complex subunit beta × 1 （P62944） Adaptor protein complex AP-2, mu1 × 1 （Q5FWI9） Tetherin,Protein Nef × 2 （C3VHQ5,Q4JGV0）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2S1_RAT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain S； PDBConstruct 1–142； UniProt 1–142

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	6owt
Deposition date deposition_date	2019-05-10
Structure title title	Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
Keywords keywords	AP, HIV, Nef, trafficking, Protein transport, viral restriction factor; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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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.

6owt__assembly_1__model_1

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

Download this curve (.dat)

6owt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6owt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.50 Å
Rg (electron density)	37.73 Å
Total Rg	38.19 Å
Atom count	11649
Residues	1575
Excluded volume	208320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6owt__assembly_1__model_1`	hexameric （6）	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	AP-2 complex subunit alpha
Molecular weight formula_weight	104286.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11649

MPAVSKGEGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVCKLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDLASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSPDLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSASTDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKVQHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSIREEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAAKTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRALLLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLEEMPPFPERESSILAKLKKKKGPSTVTDLEETKRERSIDVNGGPEPVPASTSAASTPSPSADLLGLGAVPPAPTGPPPTSGGGLLVDVFSDSASAVAPLAPGSEDNFARFVCKNNGVLFENQLLQIGLKSEFRQNLGRMFIFYGNKTSTQFLNFTPTLICADDLQTNLNLQTKPVDPTVDGGAQVQQVVNIECISDFTEAPVLNIQFRYGGTFQNVSVKLPITLNKFFQPTEMASQDFFQRWKQLSNPQQEVQNIFKAKHPMDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQMYRLTLRTSKDTVSQRLCELLSEQF

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	AP-2 complex subunit beta
Molecular weight formula_weight	66953.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Adaptor protein complex AP-2, mu1
Molecular weight formula_weight	16161.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKSQ

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Tetherin,Protein Nef
Molecular weight formula_weight	31772.4 kDa
Mutation mutation	C55A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T,N

ILYDYSRMPMGDIWKEDGDKRSKGSDEASEGSGMGGVTSKKQSKRRQGLRERLLQARGETDGYSRSRGELGKGWNLPSAEGQGYSEEQFMNTPWRNPAREGEKLKYRQQNMDDVDDDDDELVGVAVHPKVPLRAMSYKLAIDMSHFIKEKGGLEGIYYSDRRHRILDIYLEKEEGIIPDWQNYTSGPGVRYPLFFGWLWKLVPVNVSDEAQEDETHCLVHPAQTSQWDDPWGEVLAWKFDPKLAYTYEAFIRYPEEFGNDSGLSKEEVKRRLTAR

Source Source

Source organism organism	Simian immunodeficiency virus
Common name common_name	SIV
NCBI taxonomy ID ncbi_taxonomy_id	11723
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	AP-2 complex subunit sigma
Molecular weight formula_weight	17011.7 kDa
Mutation mutation	N97C, C99S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHCVSELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6owtA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	6owtB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	6owtM01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	6owtS00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	60 —

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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	—

Resolution resolution	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	159406

Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex

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

AP-2 complex subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-2 complex subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Adaptor protein complex AP-2, mu1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tetherin,Protein Nef

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tetherin,Protein Nef

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AP-2 complex subunit sigma

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

6owt__assembly_1__model_1

6owt__assembly_1__model_1 | I(q)

6owt__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 (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 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)