6mdr

Cryo-EM structure of the Ceru+32/GFP-17 protomer

Method: ELECTRON MICROSCOPY

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

Ceru+32

Aequorea victoria

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 16	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GFP_AEQVI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain a； PDBConstruct 4–233； UniProt 3–232 Author chain c； PDBConstruct 4–233； UniProt 3–232 Author chain e； PDBConstruct 4–233； UniProt 3–232 Author chain g； PDBConstruct 4–233； UniProt 3–232 Author chain i； PDBConstruct 4–233； UniProt 3–232 Author chain k； PDBConstruct 4–233； UniProt 3–232 Author chain m； PDBConstruct 4–233； UniProt 3–232 Author chain o； PDBConstruct 4–233； UniProt 3–232 Author chain b； PDBConstruct 2–232； UniProt 2–232 Author chain d； PDBConstruct 2–232； UniProt 2–232 Author chain f； PDBConstruct 2–232； UniProt 2–232 Author chain h； PDBConstruct 2–232； UniProt 2–232 Author chain j； PDBConstruct 2–232； UniProt 2–232 Author chain l； PDBConstruct 2–232； UniProt 2–232 Author chain n； PDBConstruct 2–232； UniProt 2–232 Author chain p； PDBConstruct 2–232； UniProt 2–232

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	6mdr
Deposition date deposition_date	2018-09-05
Structure title title	Cryo-EM structure of the Ceru+32/GFP-17 protomer
Keywords keywords	Supercharged protein assembly, electrostatic interactions, 16-mer, D4 symmetry, LUMINESCENT PROTEIN; LUMINESCENT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

6mdr__assembly_1__model_1

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

Download this curve (.dat)

6mdr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6mdr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.41 Å
Rg (electron density)	52.90 Å
Total Rg	53.27 Å
Atom count	29456
Residues	3696
Excluded volume	524190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6mdr__assembly_1__model_1`	hexadecameric （16）	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 (2)

Entity 1 Entity 1 polymer

Description description	Ceru+32
Molecular weight formula_weight	28425.2 kDa
Mutation mutation	;E7R, T10R, V12K, D20K, E33K, E35K, Y67W, S73A, D77K, E91K, D103K, D118R, E125K, I129R, D134K, E143R, F146G, N147I, H149D, N150K, Q158R, N165K, E173K, D191R, D198R, Q205R, N213K, T231K ;
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,c,e,g,i,k,m,o
Atom count atom_count	29456

MASKGERLFRGKVPILVELKGDVNGHKFSVRGKGKGDATNGKLTLKFICTTGKLPVPWPTLVTTLTWGVQCFARYPKHMKRHDFFKSAMPKGYVQERTISFKKDGTYKTRAEVKFEGRTLVNRIKLKGRDFKEKGNILGHKLRYNGISDKVYITADKRKNGIKAKFKIRHNVKDGSVQLADHYQQNTPIGRGPVLLPRNHYLSTRSVLSKDPKEKRDHMVLLEFVTAAGIKHGRDERYKLEHHHHHH

Source Source

Source organism organism	Aequorea victoria
Common name common_name	Jellyfish
NCBI taxonomy ID ncbi_taxonomy_id	6100
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	GFP-17
Molecular weight formula_weight	27226.2 kDa
Mutation mutation	T39D, T44D, R81E, N150E, K157D, Q158E, N165E, V194D, N199E, A228D, H232E
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b,d,f,h,j,l,n,p

MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDADNGKLDLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKEHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHEVYITADDEKNGIKAEFKIRHNVEDGSVQLADHYQQNTPIGDGPDLLPDEHYLSTQSVLSKDPNEKRDHMVLLEFVTADGITEGHHHHHHHH

Source Source

Source organism organism	Aequorea victoria
Common name common_name	Jellyfish
NCBI taxonomy ID ncbi_taxonomy_id	6100
Host organism host_organism	Escherichia coli BL21(DE3)

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	6mdra00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrb00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrc00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrd00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdre00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrf00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrg00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrh00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdri00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrj00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrk00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrl00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrm00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrn00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdro00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6mdrp00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.47 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	126822

Cryo-EM structure of the Ceru+32/GFP-17 protomer

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

Ceru+32

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

6mdr__assembly_1__model_1

6mdr__assembly_1__model_1 | I(q)

6mdr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Cryo-EM structure of the Ceru+32/GFP-17 protomer

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

Ceru+32

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

6mdr__assembly_1__model_1

6mdr__assembly_1__model_1 | I(q)

6mdr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)