SAXSdb — 8kb8

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

WD repeat-containing protein 91

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-7a × 1 （P51149） MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-7a × 1 （P51149） MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WDR91_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–357； UniProt 392–747 Author chain B； PDBConstruct 2–357； UniProt 392–747

Ras-related protein Rab-7a

Homo sapiens

UniProt P51149

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	WD repeat-containing protein 91 × 1 （A4D1P6） MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	WD repeat-containing protein 91 × 1 （A4D1P6） MAGNESIUM ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB7A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 6–181； UniProt 1–176 Author chain D； PDBConstruct 6–181； UniProt 1–176

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	8kb8
Deposition date deposition_date	2023-08-04
Structure title title	Structure of the WDR91 WD40 domain complexed with Rab7
Keywords keywords	GTPase, Effector, WD40, complex, ENDOCYTOSIS; ENDOCYTOSIS
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.

8kb8__assembly_1__model_1

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

Download this curve (.dat)

8kb8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8kb8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.57 Å
Rg (electron density)	24.81 Å
Total Rg	25.57 Å
Atom count	3986
Residues	509
Excluded volume	70888 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8kb8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8kb8__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	WD repeat-containing protein 91
Molecular weight formula_weight	39824.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7985

MPEQPFIVLGQEEYGEHHSSIMHCRVDCSGRRVASLDVDGVIKVWSFNPIMQTKASSISKSPLLSLEWATKRDRLLLLGSGVGTVRLYDTEAKKNLCEININDNMPRILSLACSPNGASFVCSAAAPSLTSQVDFSAPDIGSKGMNQVPGRLLLWDTKTMKQQLQFSLDPEPIAINCTAFNHNGNLLVTGAADGVIRLFDMQQHECAMSWRAHYGEVYSVEFSYDENTVYSIGEDGKFIQWNIHKSGLKVSEYSLPSDATGPFVLSGYSGYKQVQVPRGRLFAFDSEGNYMLTCSATGGVIYKLGGDEKVLESCLSLGGHRAPVVTVDWSTAMDCGTCLTASMDGKIKLTTLLAHKAHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-7a
Molecular weight formula_weight	20410.4 kDa
Mutation mutation	Q67L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPLGSMTSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGLERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQ

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 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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Unit-cell length a length_a	55.452 Å
Unit-cell length b length_b	81.077 Å
Unit-cell length c length_c	116.404 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.490 Å
Low-resolution limit resolution_low	48.490 Å
R factor r_factor	0.2007
R_work r_work	0.1974
R_free r_free	0.2612

Structure of the WDR91 WD40 domain complexed with Rab7

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

WD repeat-containing protein 91

State in the Current Structure

Other States of the Same Protein in the Database

Ras-related protein Rab-7a

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

8kb8__assembly_1__model_1

8kb8__assembly_1__model_1 | I(q)

8kb8__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 (5)

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 water

7. Citations (1)

Structure of the WDR91 WD40 domain complexed with Rab7

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

WD repeat-containing protein 91

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras-related protein Rab-7a

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

8kb8__assembly_1__model_1

8kb8__assembly_1__model_1 | I(q)

8kb8__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 (5)

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 water

7. Citations (1)