SAXSdb — 5iib

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

Egg-lysin

Haliotis rufescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	Vitelline envelope sperm lysin receptor × 1 （Q8WR62） beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELYS_HALRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 19–154

Vitelline envelope sperm lysin receptor

Haliotis rufescens

UniProt Q8WR62

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	Egg-lysin × 1 （P04552） beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8WR62_HALRU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–120； UniProt 340–453

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	5iib
Deposition date deposition_date	2016-03-01
Structure title title	Crystal structure of red abalone egg VERL repeat 3 in complex with sperm lysin at 1.64 A resolution (crystal form II)
Keywords keywords	;CELL ADHESION, FERTILIZATION, EGG-SPERM INTERACTION, GAMETE RECOGNITION, SPERM RECEPTOR, EGG COAT, VITELLINE ENVELOPE, ZP DOMAIN, ZP-N DOMAIN, SPERM ACROSOME, EGG COAT PENETRATION ;; CELL ADHESION
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.

5iib__assembly_1__model_1

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

Download this curve (.dat)

5iib__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5iib__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.44 Å
Rg (electron density)	18.26 Å
Total Rg	19.32 Å
Atom count	3927
Residues	232
Excluded volume	35344 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5iib__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	Egg-lysin
Molecular weight formula_weight	16295.2 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	4065

RSWHYVEPKFLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYMGK

Source Source

Source organism organism	Haliotis rufescens
Common name common_name	California red abalone
NCBI taxonomy ID ncbi_taxonomy_id	6454
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Vitelline envelope sperm lysin receptor
Molecular weight formula_weight	14432.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ETGAAADWDVYCSQDESIPAKFISRLVTSKDQALEKTEINCSNGLVPITQEFGINMMLIQYTRNELLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTNLSIQCYMPKSPVAPKLEHHHHHH

Source Source

Source organism organism	Haliotis rufescens
Common name common_name	California red abalone
NCBI taxonomy ID ncbi_taxonomy_id	6454
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Source Source

Source organism organism	Haliotis rufescens
Common name common_name	California red abalone
NCBI taxonomy ID ncbi_taxonomy_id	6454
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5iiba_
Class class	a — All alpha proteins
Fold Fold fold	a.19 — Fertilization protein
Superfamily Superfamily superfamily	a.19.1 — Fertilization protein
Family Family family	a.19.1.1 — Fertilization protein

CATH v4.4 (1 domains)

Domain ID domain_id	5iibA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	10 — Fertilization protein

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7. Citations (8)

Structural Basis of Egg Coat-Sperm Recognition at Fertilization.

Cell (2017)

PMID: 28622512 · DOI: 10.1016/j.cell.2017.05.033 PRIMARY

The molecular basis of sex: linking yeast to human.

Mol. Biol. Evol. (2011)

PMID: 21282709 · DOI: 10.1093/molbev/msr026

Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs.

Proc. Natl. Acad. Sci. U.S.A. (2006)

PMID: 17085584

Full-length sequence of VERL, the egg vitelline envelope receptor for abalone sperm lysin.

Gene (2002)

PMID: 12034500

;1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding. ;

Acta Crystallogr. D Biol. Crystallogr. (2000)

PMID: 10666624

The abalone egg vitelline envelope receptor for sperm lysin is a giant multivalent molecule.

Proc. Natl. Acad. Sci. U.S.A. (1997)

PMID: 9192632

;Crystal structure and subunit dynamics of the abalone sperm lysin dimer: egg envelopes dissociate dimers, the monomer is the active species. ;

J. Cell Biol. (1995)

PMID: 7657696

The crystal structure of lysin, a fertilization protein.

Science (1993)

PMID: 8266073

Unit-cell length a length_a	64.500 Å
Unit-cell length b length_b	64.500 Å
Unit-cell length c length_c	129.930 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.640 Å
Low-resolution limit resolution_low	32.250 Å
R factor r_factor	0.1910
R_work r_work	0.1900
R_free r_free	0.2050

Crystal structure of red abalone egg VERL repeat 3 in complex with sperm lysin at 1.64 A resolution (crystal form II)

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

Egg-lysin

State in the Current Structure

Other States of the Same Protein in the Database

Vitelline envelope sperm lysin receptor

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

5iib__assembly_1__model_1

5iib__assembly_1__model_1 | I(q)

5iib__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 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Source Source

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (8)

Crystal structure of red abalone egg VERL repeat 3 in complex with sperm lysin at 1.64 A resolution (crystal form II)

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

Egg-lysin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vitelline envelope sperm lysin receptor

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

5iib__assembly_1__model_1

5iib__assembly_1__model_1 | I(q)

5iib__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 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Source Source

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (8)