SAXSdb — 6uri

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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	Protein heterocomplex	Heteromer	Protein 6	AP-2 complex subunit sigma × 1 （P53680） Protein Nef × 1 （Q90VU7） AP-2 complex subunit beta × 1 （P63010） AP-2 complex subunit mu × 1 （Q96CW1） cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4 × 1 （B4DT49） water × 2	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 15–635； UniProt 1–621

AP-2 complex subunit sigma

Homo sapiens

UniProt P53680

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） Protein Nef × 1 （Q90VU7） AP-2 complex subunit beta × 1 （P63010） AP-2 complex subunit mu × 1 （Q96CW1） cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4 × 1 （B4DT49） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2S1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain S； PDBConstruct 1–142； UniProt 1–142

Protein Nef

Human immunodeficiency virus 1

UniProt Q90VU7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） AP-2 complex subunit sigma × 1 （P53680） AP-2 complex subunit beta × 1 （P63010） AP-2 complex subunit mu × 1 （Q96CW1） cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4 × 1 （B4DT49） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q90VU7_9HIV1
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain N； PDBConstruct 6–186； UniProt 26–206

AP-2 complex subunit beta

Homo sapiens

UniProt P63010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） AP-2 complex subunit sigma × 1 （P53680） Protein Nef × 1 （Q90VU7） AP-2 complex subunit mu × 1 （Q96CW1） cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4 × 1 （B4DT49） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2B1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 25–615； UniProt 1–591

AP-2 complex subunit mu

Homo sapiens

UniProt Q96CW1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） AP-2 complex subunit sigma × 1 （P53680） Protein Nef × 1 （Q90VU7） AP-2 complex subunit beta × 1 （P63010） cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4 × 1 （B4DT49） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2M1_HUMAN
Isoform	Q96CW1-2
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–135； UniProt 1–135

cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4

Homo sapiens

UniProt B4DT49

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	AP-2 complex subunit alpha × 1 （Q66HM2） AP-2 complex subunit sigma × 1 （P53680） Protein Nef × 1 （Q90VU7） AP-2 complex subunit beta × 1 （P63010） AP-2 complex subunit mu × 1 （Q96CW1） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B4DT49_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 37–62； UniProt 146–171

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	6uri
Deposition date deposition_date	2019-10-23
Structure title title	HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex
Keywords keywords	CD4, 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.

6uri__assembly_1__model_1

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

Download this curve (.dat)

6uri__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6uri__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.51 Å
Rg (electron density)	38.76 Å
Total Rg	39.26 Å
Atom count	12261
Residues	1531
Excluded volume	219980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6uri__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 (7)

Entity 1 Entity 1 polymer

Description description	AP-2 complex subunit alpha
Molecular weight formula_weight	72069.8 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	12263

MGSSHHHHHHSQDPMPAVSKGEGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVCKLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDLASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSPDLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSASTDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKVQHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSIREEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAAKTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRALLLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLEEMPPFPERESSILAKLKKKKGENLYFQ

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 sigma
Molecular weight formula_weight	17066.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDARHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE

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

Entity 3 Entity 3 polymer

Description description	Protein Nef
Molecular weight formula_weight	21032.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

AGFSMAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	AP-2 complex subunit beta
Molecular weight formula_weight	69473.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSQDPNSSSARLQVDMTDSKYFTTNKKGEISELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKHPNKYESIIATLCGNLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

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

Entity 5 Entity 5 polymer

Description description	AP-2 complex subunit mu
Molecular weight formula_weight	15518.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQ

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

Entity 6 Entity 6 polymer

Description description	cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4
Molecular weight formula_weight	6881.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GVDGSDEASELACPTPKEDGLAQQQTQLNLRGSGSGCVRCRHRRRQAERMSQIKRLLSEKKT

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6uria_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.10 — Clathrin adaptor core protein

Domain ID domain_id	d6urib_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.10 — Clathrin adaptor core protein

Domain ID domain_id	d6urim_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.4 — SNARE-like
Family Family family	d.110.4.2 — Clathrin coat assembly domain

Domain ID domain_id	d6uris_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.4 — SNARE-like
Family Family family	d.110.4.2 — Clathrin coat assembly domain

CATH v4.4 (3 domains)

Domain ID domain_id	6uriA01
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	6uriM01
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	6uriN01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily	10 — Nef Regulatory Factor

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Unit-cell length a length_a	109.154 Å
Unit-cell length b length_b	109.154 Å
Unit-cell length c length_c	178.915 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	4

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	tetragonal

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.820 Å
R factor r_factor	0.2419
R_work r_work	0.2410
R_free r_free	0.2768

HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor 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 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

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 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

AP-2 complex subunit mu

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4

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

6uri__assembly_1__model_1

6uri__assembly_1__model_1 | I(q)

6uri__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 (7)

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

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 water