1ltx

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid

Method: X-RAY DIFFRACTION

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

RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT × 1 （Q08603） Rab Escort Protein 1 × 1 （P37727） AAAA × 1 ZINC ION × 1 CHLORIDE ION × 1 FARNESYL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGTA_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–567； UniProt 1–567

RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT

Rattus norvegicus

UniProt Q08603

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT × 1 （Q08602） Rab Escort Protein 1 × 1 （P37727） AAAA × 1 ZINC ION × 1 CHLORIDE ION × 1 FARNESYL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGTB_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–331； UniProt 1–331

Rab Escort Protein 1

Rattus norvegicus

UniProt P37727

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT × 1 （Q08602） RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT × 1 （Q08603） AAAA × 1 ZINC ION × 1 CHLORIDE ION × 1 FARNESYL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAE1_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain R； PDBConstruct 1–650； UniProt 1–650

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	1ltx
Deposition date deposition_date	2002-05-21
Structure title title	Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid
Keywords keywords	RAB PRENYLATION, PRENYLTRANSFERASE, LUCINE-RICH REPEATS, POST-TRANSLATIONAL MODIFICATION, Transferase-Protein binding COMPLEX; Transferase/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.

1ltx__assembly_1__model_1

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

Download this curve (.dat)

1ltx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ltx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.19 Å
Rg (electron density)	40.88 Å
Total Rg	41.15 Å
Atom count	10750
Residues	1352
Excluded volume	191630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ltx__assembly_1__model_1`	tetrameric （4）	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 (8)

Entity 1 Entity 1 polymer

Description description	RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT
Molecular weight formula_weight	64981.2 kDa
EC 编号 ec_number	2.5.1.-
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	10874

MHGRLKVKTSEEQAEAKRLEREQKLKLYQSATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDVLCCVHVSREEACLSVCFSRPLTVGSRMGTLLLMVDEAPLSVEWRTPDGRNRPSHVWLCDLPAASLNDQLPQHTFRVIWTGSDSQKECVLLKDRPECWCRDSATDEQLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNLQGNSLCQEEGIQERLAEMLPSVSSILT

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT
Molecular weight formula_weight	36892.2 kDa
EC 编号 ec_number	2.5.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPEEVLQRVNVQPELVS

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Rab Escort Protein 1
Molecular weight formula_weight	72594.2 kDa
Mutation mutation	A473T, G483A, Q231K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MADNLPSDFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENNDVVTENSMWQEQILENEEAIPLSSKDKTIQHVEVFCYASQDLHKDVEEAGALQKNHASVTSAQSAEAAEAAETSCLPTAVEPLSMGSCEIPAEQSQCPGPESSPEVNDAEATGKKENSDAKSSTEEPSENVPKVQDNTETPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCVEYEEHPDEYRAYEGTTFSEYLKTQKLTPNLQYFVLHSIAMTSETTSCTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAVIDQFGQRIISKHFIIEDSYLSENTCSRVQYRQISRAVLITDGSVLKTDADQQVSILTVPAEEPGSFAVRVIELCSSTMTCMKGTYLVHLTCMSSKTAREDLERVVQKLFTPYTEIEAENEQVEKPRLLWALYFNMRDSSDISRDCYNDLPSNVYVCSGPDSGLGNDNAVKQAETLFQQICPNEDFCPAPPNPEDIVLDGDSSQQEVPESSVTPETNSETPKESTVLGNPEEPSE

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 polymer

Description description	AAAA
Molecular weight formula_weight	302.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

AAAA

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 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	FARNESYL
Molecular weight formula_weight	206.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1ltxa1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1ltxa2
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.4 — Rab geranylgeranyltransferase alpha-subunit, insert domain
Family Family family	b.7.4.1 — Rab geranylgeranyltransferase alpha-subunit, insert domain

Domain ID domain_id	d1ltxa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.2 — Rab geranylgeranyltransferase alpha-subunit, C-terminal domain

Domain ID domain_id	d1ltxb_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

Domain ID domain_id	d1ltxr1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.3 — GDI-like N domain

Domain ID domain_id	d1ltxr2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.6 — GDI-like

CATH v4.4 (7 domains)

Domain ID domain_id	1ltxA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1ltxA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1130 — Rab geranylgeranyltransferase alpha-subunit, insert domain

Domain ID domain_id	1ltxA03
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	1ltxB00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ltxR01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1ltxR02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

Domain ID domain_id	1ltxR03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

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Unit-cell length a length_a	68.700 Å
Unit-cell length b length_b	197.300 Å
Unit-cell length c length_c	85.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	19.740 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2720

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid

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

RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Rab Escort Protein 1

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

1ltx__assembly_1__model_1

1ltx__assembly_1__model_1 | I(q)

1ltx__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 (8)

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 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

CATH v4.4 (7 domains)

7. Citations (2)