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4ogr

crystal structure of P-TEFb complex with AFF4 and Tat

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

Cyclin-dependent kinase 9

Homo sapiens

UniProt P50750

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 4 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
3blh 3blq 3blr 3lq5 3mi9 3mia 3my1 3tn8 3tnh 3tni 4bcf 4bcg

34 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CDK9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–332； UniProt 1–330 Author chain E； PDBConstruct 3–332； UniProt 1–330 Author chain I； PDBConstruct 3–332； UniProt 1–330

Cyclin-T1

Homo sapiens

UniProt O60563

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 4 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
2pk2 3blh 3blq 3blr 3lq5 3mi9 3mia 3my1 3tn8 3tnh 3tni 4bcf

35 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CCNT1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–264； UniProt 1–264 Author chain F； PDBConstruct 1–264； UniProt 1–264 Author chain K； PDBConstruct 1–264； UniProt 1–264

AF4/FMR2 family member 4

Homo sapiens

UniProt Q9UHB7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） Protein Tat × 1 （P69698） ADENOSINE × 1 ZINC ION × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6kn5

1 assemblies

Homodimer
6k7p 6r80

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4imy 4imy 4imy 4ogr 4ogr 4ogr 4or5 4or5 5jw9 5l1z 5l1z 6cyt

12 assemblies

View Construct and Data Evidence
UniProt name AFF4_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 4–75； UniProt 2–73 Author chain G； PDBConstruct 4–75； UniProt 2–73 Author chain L； PDBConstruct 4–75； UniProt 2–73

Protein Tat

Human immunodeficiency virus type 1 (HXB3 ISOLATE)

UniProt P69698

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） ADENOSINE × 1 ZINC ION × 2 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） ADENOSINE × 1 ZINC ION × 2 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） ADENOSINE × 1 ZINC ION × 2 water × 4 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
4ogr 4ogr 4ogr

3 assemblies

View Construct and Data Evidence
UniProt name TAT_HV1H3
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 2–58； UniProt 1–57 Author chain H； PDBConstruct 2–58； UniProt 1–57 Author chain M； PDBConstruct 2–58； UniProt 1–57

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_id4ogr
Deposition date deposition_date2014-01-16
Structure title titlecrystal structure of P-TEFb complex with AFF4 and Tat
Keywords keywords;P-TEFb, cyclin-dependent kinase 9, cyclin fold, intrinsically unstructured AFF4, transcriptional regulation at HIV promoter, binds TAR, N-terminal acetylation of Tat, transferase-viral protein complex ;; transferase/viral protein
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.

4ogr__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4ogr__assembly_3__model_1 | I(q)

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

4ogr__assembly_3__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）29.67 Å
Rg (electron density)28.66 Å
Total Rg29.46 Å
Atom count10778
Residues676
Excluded volume96997 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4ogr__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4ogr__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4ogr__assembly_3__model_1 tetrameric （4） 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)

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6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd4ogra_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4ogrb1
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd4ogrb2
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd4ogre_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4ogrf1
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd4ogrf2
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd4ogri_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4ogrk1
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd4ogrk2
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin

CATH v4.4 (14 domains)

Domain ID domain_id4ogrA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4ogrA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4ogrB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4ogrB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4ogrC00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily2670 —
Domain ID domain_id4ogrE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4ogrE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4ogrF01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4ogrF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4ogrI01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4ogrI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4ogrK01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4ogrK02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4ogrL00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily2670 —
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7. Citations (1)