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4nee

crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit alpha-2 × 1 （Q66HM2） Protein Nef × 1 （Q90VU7） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit alpha-2 × 1 （Q66HM2） Protein Nef × 1 （Q90VU7） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit alpha-2 × 1 （Q66HM2） Protein Nef × 1 （Q90VU7） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit alpha-2 × 1 （Q66HM2） Protein Nef × 1 （Q90VU7） Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4nee 4nee 4nee 4nee 6owo 6owt 6oxl 9pwb

8 assemblies

View Construct and Data Evidence
UniProt name AP2S1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain D； PDBConstruct 1–142； UniProt 1–142 Author chain F； PDBConstruct 1–142； UniProt 1–142 Author chain I； PDBConstruct 1–142； UniProt 1–142 Author chain L； PDBConstruct 1–142； UniProt 1–142

AP-2 complex subunit alpha-2

Rattus norvegicus

UniProt Q66HM2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit sigma × 1 （P62744） Protein Nef × 1 （Q90VU7） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit sigma × 1 （P62744） Protein Nef × 1 （Q90VU7） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit sigma × 1 （P62744） Protein Nef × 1 （Q90VU7） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit sigma × 1 （P62744） Protein Nef × 1 （Q90VU7） Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2vgl 2xa7 2xa7 4nee 4nee 4nee 4nee 6owt 6qh5 6qh6 6qh7 6uri

13 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q66HM2_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 3–398； UniProt 1–396 Author chain B； PDBConstruct 3–398； UniProt 1–396 Author chain G； PDBConstruct 3–398； UniProt 1–396 Author chain J； PDBConstruct 3–398； UniProt 1–396

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 3 AP-2 complex subunit sigma × 1 （P62744） AP-2 complex subunit alpha-2 × 1 （Q66HM2） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit sigma × 1 （P62744） AP-2 complex subunit alpha-2 × 1 （Q66HM2） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit sigma × 1 （P62744） AP-2 complex subunit alpha-2 × 1 （Q66HM2） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 AP-2 complex subunit sigma × 1 （P62744） AP-2 complex subunit alpha-2 × 1 （Q66HM2） Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4emz 4emz 4en2 4en2 4nee 4nee 4nee 4nee 6cm9 6cri 6d83 6d84

26 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q90VU7_9HIV1
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 15–155； UniProt 63–203 Author chain E； PDBConstruct 15–155； UniProt 63–203 Author chain H； PDBConstruct 15–155； UniProt 63–203 Author chain K； PDBConstruct 15–155； UniProt 63–203

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_id4nee
Deposition date deposition_date2013-10-29
Structure title titlecrystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef
Keywords keywordsclathrin Adaptor AP-2, HIV-1 Nef, CD4 downregulation, VIRAL PROTEIN-PROTEIN TRANSPORT complex; VIRAL PROTEIN/PROTEIN TRANSPORT
Experimental Method methodX-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.

4nee__assembly_1__model_1

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

Download this curve (.dat)

4nee__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4nee__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）28.16 Å
Rg (electron density)27.16 Å
Total Rg27.96 Å
Atom count5380
Residues669
Excluded volume96256 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4nee__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4nee__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4nee__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 4nee__assembly_4__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 (3)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd4neec1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.102 — Regulatory factor Nef
Superfamily Superfamily superfamilyd.102.1 — Regulatory factor Nef
Family Family familyd.102.1.0 — automated matches
Domain ID domain_idd4neec2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4need_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.110 — Profilin-like
Superfamily Superfamily superfamilyd.110.4 — SNARE-like
Family Family familyd.110.4.2 — Clathrin coat assembly domain
Domain ID domain_idd4neee1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.102 — Regulatory factor Nef
Superfamily Superfamily superfamilyd.102.1 — Regulatory factor Nef
Family Family familyd.102.1.0 — automated matches
Domain ID domain_idd4neee2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4neef_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.110 — Profilin-like
Superfamily Superfamily superfamilyd.110.4 — SNARE-like
Family Family familyd.110.4.2 — Clathrin coat assembly domain
Domain ID domain_idd4neeh1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.102 — Regulatory factor Nef
Superfamily Superfamily superfamilyd.102.1 — Regulatory factor Nef
Family Family familyd.102.1.0 — automated matches
Domain ID domain_idd4neeh2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4neei_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.110 — Profilin-like
Superfamily Superfamily superfamilyd.110.4 — SNARE-like
Family Family familyd.110.4.2 — Clathrin coat assembly domain
Domain ID domain_idd4neek1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.102 — Regulatory factor Nef
Superfamily Superfamily superfamilyd.102.1 — Regulatory factor Nef
Family Family familyd.102.1.0 — automated matches
Domain ID domain_idd4neek2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4neel_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.110 — Profilin-like
Superfamily Superfamily superfamilyd.110.4 — SNARE-like
Family Family familyd.110.4.2 — Clathrin coat assembly domain

CATH v4.4 (12 domains)

Domain ID domain_id4neeA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id4neeB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id4neeC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily10 — Nef Regulatory Factor
Domain ID domain_id4neeD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily60 —
Domain ID domain_id4neeE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily10 — Nef Regulatory Factor
Domain ID domain_id4neeF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily60 —
Domain ID domain_id4neeG00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id4neeH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily10 — Nef Regulatory Factor
Domain ID domain_id4neeI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily60 —
Domain ID domain_id4neeJ00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id4neeK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily10 — Nef Regulatory Factor
Domain ID domain_id4neeL00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily60 —
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7. Citations (1)