4fl4

Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome

Method: X-RAY DIFFRACTION

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

Glycoside hydrolase family 9

Clostridium thermocellum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Scaffolding dockerin binding protein A × 1 （P71143） Cellulosome anchoring protein cohesin region × 1 （C7HJU1） CALCIUM ION × 4 SULFATE ION × 13 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Scaffolding dockerin binding protein A × 1 （P71143） Cellulosome anchoring protein cohesin region × 1 （C7HJU1） CALCIUM ION × 4 SULFATE ION × 18 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Scaffolding dockerin binding protein A × 1 （P71143） Cellulosome anchoring protein cohesin region × 1 （C7HJU1） CALCIUM ION × 4 SULFATE ION × 13 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Scaffolding dockerin binding protein A × 1 （P71143） Cellulosome anchoring protein cohesin region × 1 （C7HJU1） CALCIUM ION × 4 SULFATE ION × 14 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D1NID1_CLOTM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–88； UniProt 584–649 Author chain D； PDBConstruct 23–88； UniProt 584–649 Author chain G； PDBConstruct 23–88； UniProt 584–649 Author chain J； PDBConstruct 23–88； UniProt 584–649

Scaffolding dockerin binding protein A

Clostridium thermocellum

UniProt P71143

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Glycoside hydrolase family 9 × 1 （D1NID1） Cellulosome anchoring protein cohesin region × 1 （C7HJU1） CALCIUM ION × 4 SULFATE ION × 13 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Glycoside hydrolase family 9 × 1 （D1NID1） Cellulosome anchoring protein cohesin region × 1 （C7HJU1） CALCIUM ION × 4 SULFATE ION × 18 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Glycoside hydrolase family 9 × 1 （D1NID1） Cellulosome anchoring protein cohesin region × 1 （C7HJU1） CALCIUM ION × 4 SULFATE ION × 13 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Glycoside hydrolase family 9 × 1 （D1NID1） Cellulosome anchoring protein cohesin region × 1 （C7HJU1） CALCIUM ION × 4 SULFATE ION × 14 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P71143_CLOTM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 14–187； UniProt 27–200 Author chain E； PDBConstruct 14–187； UniProt 27–200 Author chain H； PDBConstruct 14–187； UniProt 27–200 Author chain K； PDBConstruct 14–187； UniProt 27–200

Cellulosome anchoring protein cohesin region

Clostridium thermocellum

UniProt C7HJU1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Glycoside hydrolase family 9 × 1 （D1NID1） Scaffolding dockerin binding protein A × 1 （P71143） CALCIUM ION × 4 SULFATE ION × 13 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Glycoside hydrolase family 9 × 1 （D1NID1） Scaffolding dockerin binding protein A × 1 （P71143） CALCIUM ION × 4 SULFATE ION × 18 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Glycoside hydrolase family 9 × 1 （D1NID1） Scaffolding dockerin binding protein A × 1 （P71143） CALCIUM ION × 4 SULFATE ION × 13 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Glycoside hydrolase family 9 × 1 （D1NID1） Scaffolding dockerin binding protein A × 1 （P71143） CALCIUM ION × 4 SULFATE ION × 14 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C7HJU1_CLOTM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–313； UniProt 9–320 Author chain F； PDBConstruct 2–313； UniProt 9–320 Author chain I； PDBConstruct 2–313； UniProt 9–320 Author chain L； PDBConstruct 2–313； UniProt 9–320

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	4fl4
Deposition date deposition_date	2012-06-14
Structure title title	Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome
Keywords keywords	;Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, cohesin, dockerin, X module, cell surface, hydrolase, PROTEIN BINDING ;; PROTEIN BINDING
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.

4fl4__assembly_1__model_1

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

Download this curve (.dat)

4fl4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4fl4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.25 Å
Rg (electron density)	45.13 Å
Total Rg	45.02 Å
Atom count	4052
Residues	541
Excluded volume	72045 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4fl4__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4fl4__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4fl4__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4fl4__assembly_4__model_1`	trimeric （3）	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	Glycoside hydrolase family 9
Molecular weight formula_weight	9948.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	16313

MGHHHHHHHHHHSSGHIEGRHMGDVNDDGKVNSTDLTLLKRYVLKAVSTLPSSKAEKNADVNRDGRVNSSDVTILSRYLIRVIEKLPI

Source Source

Source organism organism	Clostridium thermocellum
NCBI taxonomy ID ncbi_taxonomy_id	1515
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Scaffolding dockerin binding protein A
Molecular weight formula_weight	20550.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

MRGSHHHHHHTDLRADKASSIELKFDRNKGEVGDILIGTVRINNIKNFAGFQVNIVYDPKVLMAVDPETGKEFTSSTFPPGRTVLKNNAYGPIQIADNDPEKGILNFALAYSYIAGYKETGVAEESGIIAKIGFKILQKKSTAVKFQDTLSMPGAISGTQLFDWDGEVITGYEVIQPDVLSLGDEPF

Source Source

Source organism organism	Clostridium thermocellum
NCBI taxonomy ID ncbi_taxonomy_id	1515
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Cellulosome anchoring protein cohesin region
Molecular weight formula_weight	34659.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

MPTITPNKLTLKIGRAEGRPGDTVEIPVNLYGVPQKGIASGDFVVSYDPNVLEIIEIEPGELIVDPNPTKSFDTAVYPDRKMIVFLFAEDSGTGAYAITEDGVFATIVAKVKEGAPEGFSAIEISEFGAFADNDLVEVETDLINGGVLVTNKPVIEGYKVSGYILPDFSFDATVAPLVKAGFKVEIVGTELYAVTDANGYFEITGVPANASGYTLKISRATYLDRVIANVVVTGDTSVSTSQAPIMMWVGDIVKDNSINLLDVAEVIRCFNATKGSANYVEELDINRNGAINMQDIMIVHKHFGATSSDYDAQLEHHHHHH

Source Source

Source organism organism	Clostridium thermocellum
NCBI taxonomy ID ncbi_taxonomy_id	1515
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	58

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4fl4a1
Class class	a — All alpha proteins
Fold Fold fold	a.139 — Type I dockerin domain
Superfamily Superfamily superfamily	a.139.1 — Type I dockerin domain
Family Family family	a.139.1.0 — automated matches

Domain ID domain_id	d4fl4a2
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

Domain ID domain_id	d4fl4b_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.2 — Carbohydrate-binding domain
Family Family family	b.2.2.2 — Cellulose-binding domain family III

Domain ID domain_id	d4fl4d1
Class class	a — All alpha proteins
Fold Fold fold	a.139 — Type I dockerin domain
Superfamily Superfamily superfamily	a.139.1 — Type I dockerin domain
Family Family family	a.139.1.0 — automated matches

Domain ID domain_id	d4fl4d2
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

Domain ID domain_id	d4fl4e_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.2 — Carbohydrate-binding domain
Family Family family	b.2.2.2 — Cellulose-binding domain family III

Domain ID domain_id	d4fl4g1
Class class	a — All alpha proteins
Fold Fold fold	a.139 — Type I dockerin domain
Superfamily Superfamily superfamily	a.139.1 — Type I dockerin domain
Family Family family	a.139.1.0 — automated matches

Domain ID domain_id	d4fl4g2
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

Domain ID domain_id	d4fl4h_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.2 — Carbohydrate-binding domain
Family Family family	b.2.2.2 — Cellulose-binding domain family III

Domain ID domain_id	d4fl4j1
Class class	a — All alpha proteins
Fold Fold fold	a.139 — Type I dockerin domain
Superfamily Superfamily superfamily	a.139.1 — Type I dockerin domain
Family Family family	a.139.1.0 — automated matches

Domain ID domain_id	d4fl4j2
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

Domain ID domain_id	d4fl4k_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.2 — Carbohydrate-binding domain
Family Family family	b.2.2.2 — Cellulose-binding domain family III

CATH v4.4 (18 domains)

Domain ID domain_id	4fl4A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1330 — Type 1 dockerin domain
Homologous superfamily homologous superfamily	10 — Dockerin domain

Domain ID domain_id	4fl4B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4fl4C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4fl4C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1120 — Carboxypeptidase-like, regulatory domain

Domain ID domain_id	4fl4C03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1330 — Type 1 dockerin domain
Homologous superfamily homologous superfamily	10 — Dockerin domain

Domain ID domain_id	4fl4D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1330 — Type 1 dockerin domain
Homologous superfamily homologous superfamily	10 — Dockerin domain

Domain ID domain_id	4fl4E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4fl4F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4fl4F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	4130 —

Domain ID domain_id	4fl4G00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1330 — Type 1 dockerin domain
Homologous superfamily homologous superfamily	10 — Dockerin domain

Domain ID domain_id	4fl4H00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4fl4I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4fl4I02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1120 — Carboxypeptidase-like, regulatory domain

Domain ID domain_id	4fl4I03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1330 — Type 1 dockerin domain
Homologous superfamily homologous superfamily	10 — Dockerin domain

Domain ID domain_id	4fl4J00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1330 — Type 1 dockerin domain
Homologous superfamily homologous superfamily	10 — Dockerin domain

Domain ID domain_id	4fl4K00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4fl4L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	4fl4L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	4130 —

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Unit-cell length a length_a	119.374 Å
Unit-cell length b length_b	186.305 Å
Unit-cell length c length_c	191.165 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	16

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.947 Å
R factor r_factor	0.1932
R_work r_work	0.1909
R_free r_free	0.2363

Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome

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

Glycoside hydrolase family 9

State in the Current Structure

Other States of the Same Protein in the Database

Scaffolding dockerin binding protein A

State in the Current Structure

Other States of the Same Protein in the Database

Cellulosome anchoring protein cohesin region

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

4fl4__assembly_1__model_1

4fl4__assembly_1__model_1 | I(q)

4fl4__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. Citations (1)

Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome

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

Glycoside hydrolase family 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

Scaffolding dockerin binding protein A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cellulosome anchoring protein cohesin region

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

4fl4__assembly_1__model_1

4fl4__assembly_1__model_1 | I(q)

4fl4__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. Citations (1)