4or5

Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4

Method: X-RAY DIFFRACTION

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

Cyclin-dependent kinase 9

Homo sapiens

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） Protein Tat × 1 （P04608） AF4/FMR2 family member 4 × 1 （Q9UHB7） YTTRIUM (III) ION × 8 SULFATE ION × 2 ZINC ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-T1 × 1 （O60563） Protein Tat × 1 （P04608） AF4/FMR2 family member 4 × 1 （Q9UHB7） YTTRIUM (III) ION × 8 SULFATE ION × 2 ZINC ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDK9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 7–332 Author chain F； PDBConstruct 1–326； UniProt 7–332

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） Protein Tat × 1 （P04608） AF4/FMR2 family member 4 × 1 （Q9UHB7） YTTRIUM (III) ION × 8 SULFATE ION × 2 ZINC ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-dependent kinase 9 × 1 （P50750） Protein Tat × 1 （P04608） AF4/FMR2 family member 4 × 1 （Q9UHB7） YTTRIUM (III) ION × 8 SULFATE ION × 2 ZINC ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCNT1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–266； UniProt 1–266 Author chain G； PDBConstruct 1–266； UniProt 1–266

Protein Tat

HIV-1

UniProt P04608

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） YTTRIUM (III) ION × 8 SULFATE ION × 2 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） YTTRIUM (III) ION × 8 SULFATE ION × 2 ZINC ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TAT_HV1H2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–48； UniProt 1–48 Author chain H； PDBConstruct 1–48； UniProt 1–48

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 （P04608） YTTRIUM (III) ION × 8 SULFATE ION × 2 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 （P04608） YTTRIUM (III) ION × 8 SULFATE ION × 2 ZINC ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AFF4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 6–43； UniProt 32–69 Author chain J； PDBConstruct 6–43； UniProt 32–69

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	4or5
Deposition date deposition_date	2014-02-10
Structure title title	Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4
Keywords keywords	Cdk9, Tat, AFF4, Zinc Finger, Transcription, RNA binding, Phosphorylation, Transferase-Transcription complex; Transferase/Transcription
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.

4or5__assembly_1__model_1

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

Download this curve (.dat)

4or5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4or5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.72 Å
Rg (electron density)	28.77 Å
Total Rg	29.60 Å
Atom count	5379
Residues	661
Excluded volume	96574 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4or5__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4or5__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	Cyclin-dependent kinase 9
Molecular weight formula_weight	37544.6 kDa
EC 编号 ec_number	2.7.11.22, 2.7.11.23
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	10895

SVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLSTHL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 2 Entity 2 polymer

Description description	Cyclin-T1
Molecular weight formula_weight	30877.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G

MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWRACEAAKK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 3 Entity 3 polymer

Description description	Protein Tat
Molecular weight formula_weight	5428.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYG

Source Source

Source organism organism	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11706

Entity 4 Entity 4 polymer

Description description	AF4/FMR2 family member 4
Molecular weight formula_weight	4887.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J

EQIGGSPLFAEPYKVTSKEDKLSSRIQSMLGNYDEMKDFIGDR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 5 Entity 5 non-polymer

Description description	YTTRIUM (III) ION
Molecular weight formula_weight	88.9 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4or5a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d4or5b1
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d4or5b2
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d4or5f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d4or5g1
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d4or5g2
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

CATH v4.4 (8 domains)

Domain ID domain_id	4or5A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	4or5A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4or5B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4or5B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4or5F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	4or5F02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4or5G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4or5G02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

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Unit-cell length a length_a	166.862 Å
Unit-cell length b length_b	186.739 Å
Unit-cell length c length_c	108.661 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	120.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	41.900 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2670

Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4

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

Cyclin-dependent kinase 9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cyclin-T1

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 Tat

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AF4/FMR2 family member 4

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

4or5__assembly_1__model_1

4or5__assembly_1__model_1 | I(q)

4or5__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 polymer

Polymer Polymer

Source Source

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) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)