2nxp

Structure of NTD2 domain of the human TAF5 subunit of TFIID

Method: X-RAY DIFFRACTION

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

Transcription initiation factor TFIID subunit 5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TAF5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 188–343 Author chain B； PDBConstruct 1–156； UniProt 188–343 Author chain C； PDBConstruct 1–156； UniProt 188–343 Author chain D； PDBConstruct 1–156； UniProt 188–343 Author chain E； PDBConstruct 1–156； UniProt 188–343 Author chain F； PDBConstruct 1–156； UniProt 188–343 Author chain G； PDBConstruct 1–156； UniProt 188–343 Author chain H； PDBConstruct 1–156； UniProt 188–343

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	2nxp
Deposition date deposition_date	2006-11-17
Structure title title	Structure of NTD2 domain of the human TAF5 subunit of TFIID
Keywords keywords	Transcription factor, TFIID subunit, TAF5, TRANSCRIPTION; 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.

2nxp__assembly_1__model_1

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

Download this curve (.dat)

2nxp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nxp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.43 Å
Rg (electron density)	15.00 Å
Total Rg	16.18 Å
Atom count	1264
Residues	145
Excluded volume	22386 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nxp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nxp__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2nxp__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2nxp__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2nxp__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2nxp__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2nxp__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2nxp__assembly_8__model_1`	monomeric （1）	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)

Entity 1 Entity 1 polymer

Description description	Transcription initiation factor TFIID subunit 5
Molecular weight formula_weight	18842.4 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	10515

GSVAVEDQPDVSAVLSAYNQQGDPTMYEEYYSGLKHFIECSLDCHRAELSQLFYPLFVHMYLELVYNQHENEAKSFFEKFHGDQECYYQDDLRVLSSLTKKEHMKGNETMLDFRTSKFVLRISRDSYQLLKRHLQEKQNNQIWNIVQEHLYIDIFD

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 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	521

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2nxpa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

Domain ID domain_id	d2nxpb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

Domain ID domain_id	d2nxpc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

Domain ID domain_id	d2nxpd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

Domain ID domain_id	d2nxpe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

Domain ID domain_id	d2nxpf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

Domain ID domain_id	d2nxpg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

Domain ID domain_id	d2nxph_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.379 — Taf5 N-terminal domain-like
Superfamily Superfamily superfamily	d.379.1 — Taf5 N-terminal domain-like
Family Family family	d.379.1.1 — Taf5 N-terminal domain-like

CATH v4.4 (8 domains)

Domain ID domain_id	2nxpA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

Domain ID domain_id	2nxpB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

Domain ID domain_id	2nxpC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

Domain ID domain_id	2nxpD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

Domain ID domain_id	2nxpE00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

Domain ID domain_id	2nxpF00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

Domain ID domain_id	2nxpG00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

Domain ID domain_id	2nxpH00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	500 — TFIID subunit TAF5, NTD2 domain

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Unit-cell length a length_a	93.620 Å
Unit-cell length b length_b	61.829 Å
Unit-cell length c length_c	133.357 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.170 Å
Low-resolution limit resolution_low	64.420 Å
R factor r_factor	0.2151
R_work r_work	0.2126
R_free r_free	0.2625

Structure of NTD2 domain of the human TAF5 subunit of TFIID

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

Transcription initiation factor TFIID subunit 5

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

2nxp__assembly_1__model_1

2nxp__assembly_1__model_1 | I(q)

2nxp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of NTD2 domain of the human TAF5 subunit of TFIID

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

Transcription initiation factor TFIID subunit 5

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

2nxp__assembly_1__model_1

2nxp__assembly_1__model_1 | I(q)

2nxp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)