1m2o

Crystal Structure of the Sec23-Sar1 complex

Method: X-RAY DIFFRACTION

▼

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

protein transport protein SEC23

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	GTP-binding protein SAR1 × 2 （P20606） ZINC ION × 2 MAGNESIUM ION × 2 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	GTP-binding protein SAR1 × 1 （P20606） ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	GTP-binding protein SAR1 × 1 （P20606） ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC23_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–768； UniProt 1–768 Author chain C； PDBConstruct 1–768； UniProt 1–768

GTP-binding protein SAR1

Saccharomyces cerevisiae

UniProt P20606

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	protein transport protein SEC23 × 2 （P15303） ZINC ION × 2 MAGNESIUM ION × 2 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	protein transport protein SEC23 × 1 （P15303） ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	protein transport protein SEC23 × 1 （P15303） ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAR1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–190； UniProt 1–190 Author chain D； PDBConstruct 1–190； UniProt 1–190

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	1m2o
Deposition date deposition_date	2002-06-24
Structure title title	Crystal Structure of the Sec23-Sar1 complex
Keywords keywords	zinc-finger, beta barrel, vWA domain, gelsolin domain, PROTEIN TRANSPORT-SIGNALING PROTEIN COMPLEX; PROTEIN TRANSPORT/SIGNALING PROTEIN
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.

1m2o__assembly_1__model_1

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

Download this curve (.dat)

1m2o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m2o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.67 Å
Rg (electron density)	46.41 Å
Total Rg	46.57 Å
Atom count	13952
Residues	1758
Excluded volume	248440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m2o__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m2o__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1m2o__assembly_3__model_1`	dimeric （2）	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	protein transport protein SEC23
Molecular weight formula_weight	85463.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	14123

MDFETNEDINGVRFTWNVFPSTRSDANSNVVPVGCLYTPLKEYDELNVAPYNPVVCSGPHCKSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPVTVPPIFFFVVDLTSETENLDSLKESIITSLSLLPPNALIGLITYGNVVQLHDLSSETIDRCNVFRGDREYQLEALTEMLTGQKPTGPGGAASHLPNAMNKVTPFSLNRFFLPLEQVEFKLNQLLENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCYKNIPARIILFASGPGTVAPGLIVNSELKDPLRSHHDIDSDHAQHYKKACKFYNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQLTDSTGGVLLLTDAFSTAIFKQSYLRLFAKDEEGYLKMAFNGNMAVKTSKDLKVQGLIGHASAVKKTDANNISESEIGIGATSTWKMASLSPYHSYAIFFEIANTAANSNPMMSAPGSADRPHLAYTQFITTYQHSSGTNRIRVTTVANQLLPFGTPAIAASFDQEAAAVLMARIAVHKAETDDGADVIRWLDRTLIKLCQKYADYNKDDPQSFRLAPNFSLYPQFTYYLRRSQFLSVFNNSPDETAFYRHIFTREDTTNSLIMIQPTLTSFSMEDDPQPVLLDSISVKPNTILLLDTFFFILIYHGEQIAQWRKAGYQDDPQYADFKALLEEPKLEAAELLVDRFPLPRFIDTEAGGSQARFLLSKLNPSDNYQDMARGGSTIVLTDDVSLQNFMTHLQQVAVSGQA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	GTP-binding protein SAR1
Molecular weight formula_weight	21472.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MAGWDIFGWFRDVLASLGLWNKHGKLLFLGLDNAGKTTLLHMLKNDRLATLQPTWHPTSEELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPNAVSEAELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYLEAFQWLSQYI

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

▼

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1m2oa1
Class class	a — All alpha proteins
Fold Fold fold	a.71 — ERP29 C domain-like
Superfamily Superfamily superfamily	a.71.2 — Helical domain of Sec23/24
Family Family family	a.71.2.1 — Helical domain of Sec23/24

Domain ID domain_id	d1m2oa2
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.8 — beta-sandwich domain of Sec23/24
Family Family family	b.2.8.1 — beta-sandwich domain of Sec23/24

Domain ID domain_id	d1m2oa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.62 — vWA-like
Superfamily Superfamily superfamily	c.62.1 — vWA-like
Family Family family	c.62.1.2 — Trunk domain of Sec23/24

Domain ID domain_id	d1m2oa4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.2 — C-terminal, gelsolin-like domain of Sec23/24
Family Family family	d.109.2.1 — C-terminal, gelsolin-like domain of Sec23/24

Domain ID domain_id	d1m2oa5
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.10 — Zn-finger domain of Sec23/24
Family Family family	g.41.10.1 — Zn-finger domain of Sec23/24

Domain ID domain_id	d1m2ob_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d1m2oc1
Class class	a — All alpha proteins
Fold Fold fold	a.71 — ERP29 C domain-like
Superfamily Superfamily superfamily	a.71.2 — Helical domain of Sec23/24
Family Family family	a.71.2.1 — Helical domain of Sec23/24

Domain ID domain_id	d1m2oc2
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.8 — beta-sandwich domain of Sec23/24
Family Family family	b.2.8.1 — beta-sandwich domain of Sec23/24

Domain ID domain_id	d1m2oc3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.62 — vWA-like
Superfamily Superfamily superfamily	c.62.1 — vWA-like
Family Family family	c.62.1.2 — Trunk domain of Sec23/24

Domain ID domain_id	d1m2oc4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.2 — C-terminal, gelsolin-like domain of Sec23/24
Family Family family	d.109.2.1 — C-terminal, gelsolin-like domain of Sec23/24

Domain ID domain_id	d1m2oc5
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.10 — Zn-finger domain of Sec23/24
Family Family family	g.41.10.1 — Zn-finger domain of Sec23/24

Domain ID domain_id	d1m2od_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (12 domains)

Domain ID domain_id	1m2oA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1670 — beta-sandwich domain of Sec23/24

Domain ID domain_id	1m2oA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	380 — Zn-finger domain of Sec23/24

Domain ID domain_id	1m2oA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	1m2oA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	730 — Sec23/Sec24 helical domain

Domain ID domain_id	1m2oA05
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1m2oB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1m2oC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1670 — beta-sandwich domain of Sec23/24

Domain ID domain_id	1m2oC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	380 — Zn-finger domain of Sec23/24

Domain ID domain_id	1m2oC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	1m2oC04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	730 — Sec23/Sec24 helical domain

Domain ID domain_id	1m2oC05
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1m2oD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

▶

Unit-cell length a length_a	47.196 Å
Unit-cell length b length_b	151.158 Å
Unit-cell length c length_c	271.625 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	8

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	23.850 Å
R factor r_factor	0.2380
R_work r_work	0.2380
R_free r_free	0.2940

Crystal Structure of the Sec23-Sar1 complex

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

protein transport protein SEC23

State in the Current Structure

Other States of the Same Protein in the Database

GTP-binding protein SAR1

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

1m2o__assembly_1__model_1

1m2o__assembly_1__model_1 | I(q)

1m2o__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of the Sec23-Sar1 complex

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

protein transport protein SEC23

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GTP-binding protein SAR1

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

1m2o__assembly_1__model_1

1m2o__assembly_1__model_1 | I(q)

1m2o__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)