SAXSdb — 6cyt

▼

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–RNA	Heteromer	Protein 4 RNA 1	Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （A0A0C5HAL9） ;RNA (5'-R(PAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCP*U)-3') ; × 1 ZINC ION × 2	Consistent with all polymers

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 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–RNA	Heteromer	Protein 4 RNA 1	Cyclin-dependent kinase 9 × 1 （P50750） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （A0A0C5HAL9） ;RNA (5'-R(PAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCP*U)-3') ; × 1 ZINC ION × 2	Consistent with all polymers

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 1–264； 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–RNA	Heteromer	Protein 4 RNA 1	Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） Protein Tat × 1 （A0A0C5HAL9） ;RNA (5'-R(PAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCP*U)-3') ; × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AFF4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–36； UniProt 32–67

Protein Tat

Human immunodeficiency virus 1

UniProt A0A0C5HAL9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） ;RNA (5'-R(PAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCP*U)-3') ; × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0C5HAL9_9HIV1
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6cyt
Deposition date deposition_date	2018-04-06
Structure title title	HIV-1 TAR loop in complex with Tat:AFF4:P-TEFb
Keywords keywords	RNA binding protein, HIV-1 Tat, transcription elongation, HIV-1 TAR, TRANSCRIPTION, TRANSCRIPTION-RNA complex; TRANSCRIPTION/RNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6cyt__assembly_1__model_1

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

Download this curve (.dat)

6cyt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cyt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.58 Å
Rg (electron density)	30.19 Å
Total Rg	30.92 Å
Atom count	5621
Residues	669
Excluded volume	99280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cyt__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cyclin-dependent kinase 9
Molecular weight formula_weight	38226.3 kDa
EC 编号 ec_number	2.7.11.22,2.7.11.23
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	5621

GHMAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLST

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera aff. frugiperda 2 RZ-2014

Entity 2 Entity 2 polymer

Description description	Cyclin-T1
Molecular weight formula_weight	30619.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWRACEAA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera aff. frugiperda 2 RZ-2014

Entity 3 Entity 3 polymer

Description description	AF4/FMR2 family member 4
Molecular weight formula_weight	4164.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SPLFAEPYKVTSKEDYLSSRIQSMLGNYDEMKDFIG

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 4 Entity 4 polymer

Description description	Protein Tat
Molecular weight formula_weight	6784.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

XMEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRR

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Spodoptera aff. frugiperda 2 RZ-2014

Entity 5 Entity 5 polymer

Description description	;RNA (5'-R(PAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCP*U)-3') ;
Molecular weight formula_weight	6438.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	N

GAUCUGAGCCUGGGAGCUCA

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6cytA01
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	6cytA02
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	6cytB01
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	6cytB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

▶

Unit-cell length a length_a	148.580 Å
Unit-cell length b length_b	148.580 Å
Unit-cell length c length_c	104.630 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	128.674 Å
R factor r_factor	0.2510
R_work r_work	0.2475
R_free r_free	0.2829

HIV-1 TAR loop in complex with Tat:AFF4:P-TEFb

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6cyt__assembly_1__model_1

6cyt__assembly_1__model_1 | I(q)

6cyt__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 (6)

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

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)