SAXSdb — 5l1z

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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–RNA	Heteromer	Protein 4 RNA 1	Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69697） ;RNA (5'-R(PAPGPAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCPUPCPUPCP*U)-3') ; × 1 ZINC ION × 2	Consistent with all polymers
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69697） ZINC ION × 2	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 1–330； 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 （P69697） ;RNA (5'-R(PAPGPAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCPUPCPUPCP*U)-3') ; × 1 ZINC ION × 2	Consistent with all polymers
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-dependent kinase 9 × 1 （P50750） AF4/FMR2 family member 4 × 1 （Q9UHB7） Protein Tat × 1 （P69697） ZINC ION × 2	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 1–264； UniProt 1–264

AF4/FMR2 family member 4

OrganismNot specified

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 （P69697） ;RNA (5'-R(PAPGPAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCPUPCPUPCP*U)-3') ; × 1 ZINC ION × 2	Consistent with all polymers
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） Protein Tat × 1 （P69697） ZINC ION × 2	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–36； UniProt 32–67

Protein Tat

Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

UniProt P69697

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(PAPGPAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCPUPCPUPCP*U)-3') ; × 1 ZINC ION × 2	Consistent with all polymers
2	Protein heterocomplex	Heteromer	Protein 4	Cyclin-dependent kinase 9 × 1 （P50750） Cyclin-T1 × 1 （O60563） AF4/FMR2 family member 4 × 1 （Q9UHB7） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TAT_HV1B1
Isoform	P69697-2
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5l1z
Deposition date deposition_date	2016-07-29
Structure title title	TAR complex with HIV-1 Tat-AFF4-P-TEFb
Keywords keywords	HIV-1 TAR, protein-RNA complex, transcription, protein kinase, transcription-RNA complex; transcription/RNA
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.

5l1z__assembly_1__model_1

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

Download this curve (.dat)

5l1z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5l1z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.67 Å
Rg (electron density)	30.36 Å
Total Rg	31.10 Å
Atom count	5713
Residues	669
Excluded volume	100770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5l1z__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5l1z__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5l1z__assembly_3__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	Cyclin-dependent kinase 9
Molecular weight formula_weight	38031.1 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	5713

MAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLST

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

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 frugiperda

Entity 3 Entity 3 polymer

Description description	AF4/FMR2 family member 4
Molecular weight formula_weight	4130.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SPLFAEPYKVTSKEDKLSSRIQSMLGNYDEMKDFIG

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 type 1 group M subtype B (isolate BH10)
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11678
Host organism host_organism	Spodoptera frugiperda

Entity 5 Entity 5 polymer

Description description	;RNA (5'-R(PAPGPAPUPCPUPGPAPGPCPCPUPGPGPGPAPGPCPUPCPUPCP*U)-3') ;
Molecular weight formula_weight	7356.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	N

AGAUCUGAGCCUGGGAGCUCUCU

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

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Unit-cell length a length_a	146.870 Å
Unit-cell length b length_b	146.870 Å
Unit-cell length c length_c	103.750 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	5.900 Å
Low-resolution limit resolution_low	500.000 Å
R factor r_factor	—
R_work r_work	0.2169
R_free r_free	0.3132

TAR complex with HIV-1 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

Cyclin-T1

State in the Current Structure

Other States of the Same Protein in the Database

AF4/FMR2 family member 4

State in the Current Structure

Other States of the Same Protein in the Database

Protein Tat

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5l1z__assembly_1__model_1

5l1z__assembly_1__model_1 | I(q)

5l1z__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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

TAR complex with HIV-1 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

5l1z__assembly_1__model_1

5l1z__assembly_1__model_1 | I(q)

5l1z__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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)