SAXSdb — 4zn3

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

Transcription elongation factor Spt5

Methanocaldococcus jannaschii DSM 2661

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Transcription elongation factor Spt4 × 1 （Q57839） GLYCEROL × 2 FE (III) ION × 2 ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPT5_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–147； UniProt 1–147

Transcription elongation factor Spt4

Methanocaldococcus jannaschii DSM 2661

UniProt Q57839

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Transcription elongation factor Spt5 × 1 （Q57818） GLYCEROL × 2 FE (III) ION × 2 ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPT4_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 15–72； UniProt 2–59

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	4zn3
Deposition date deposition_date	2015-05-04
Structure title title	Crystal Structure of MjSpt4:Spt5 complex conformation B
Keywords keywords	protein-protein complex, 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.

4zn3__assembly_1__model_1

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

Download this curve (.dat)

4zn3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4zn3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.32 Å
Rg (electron density)	19.79 Å
Total Rg	20.57 Å
Atom count	1649
Residues	214
Excluded volume	29897 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4zn3__assembly_1__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	Transcription elongation factor Spt5
Molecular weight formula_weight	16158.9 kDa
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	1693

MIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTPKKIIENIEKGDVVEIIAGPFKGERAKVIRVDKHKEEVTLELENAAVPIPITLPVEGVKIVSKHKD

Source Source

Source organism organism	Methanocaldococcus jannaschii DSM 2661
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Transcription elongation factor Spt4
Molecular weight formula_weight	8075.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSQDPRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE

Source Source

Source organism organism	Methanocaldococcus jannaschii DSM 2661
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4zn3b1
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.9 — RNA polymerase subunits
Family Family family	g.41.9.0 — automated matches

Domain ID domain_id	d4zn3b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	4zn3A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	940 — NusG, N-terminal domain

Domain ID domain_id	4zn3A02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4zn3B00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	90 —

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Unit-cell length a length_a	45.395 Å
Unit-cell length b length_b	88.943 Å
Unit-cell length c length_c	91.955 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2288
R_work r_work	0.2274
R_free r_free	0.2557

Crystal Structure of MjSpt4:Spt5 complex conformation B

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

Transcription elongation factor Spt5

State in the Current Structure

Other States of the Same Protein in the Database

Transcription elongation factor Spt4

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

4zn3__assembly_1__model_1

4zn3__assembly_1__model_1 | I(q)

4zn3__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of MjSpt4:Spt5 complex conformation B

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

Transcription elongation factor Spt5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcription elongation factor Spt4

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

4zn3__assembly_1__model_1

4zn3__assembly_1__model_1 | I(q)

4zn3__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)