8ykd

Cryo-EM structure of ADGRG2-Gs complex with NTF nanobody

Method: ELECTRON MICROSCOPY

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

Guanine nucleotide-binding protein G(s) subunit alpha

Spodoptera

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 （P62871） Guanine nucleotide-binding protein subunit gamma × 1 （A0A7J7XNR4） Nanobody-35 × 1 Adhesion G-protein coupled receptor G2 × 1 （Q8CJ12） ScFv-16 × 1 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GNAS_CANLF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 181–361； UniProt 204–394

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Spodoptera

UniProt P62871

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Guanine nucleotide-binding protein G(s) subunit alpha × 1 （P63091） Guanine nucleotide-binding protein subunit gamma × 1 （A0A7J7XNR4） Nanobody-35 × 1 Adhesion G-protein coupled receptor G2 × 1 （Q8CJ12） ScFv-16 × 1 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GBB1_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 20–358； UniProt 2–340

Guanine nucleotide-binding protein subunit gamma

Spodoptera

UniProt A0A7J7XNR4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Guanine nucleotide-binding protein G(s) subunit alpha × 1 （P63091） Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 （P62871） Nanobody-35 × 1 Adhesion G-protein coupled receptor G2 × 1 （Q8CJ12） ScFv-16 × 1 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7J7XNR4_RHIFE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 28–108； UniProt 19–99

Adhesion G-protein coupled receptor G2

Spodoptera

UniProt Q8CJ12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Guanine nucleotide-binding protein G(s) subunit alpha × 1 （P63091） Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 （P62871） Guanine nucleotide-binding protein subunit gamma × 1 （A0A7J7XNR4） Nanobody-35 × 1 ScFv-16 × 1 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AGRG2_MOUSE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain R； PDBConstruct 25–878； UniProt 38–891

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	8ykd
Deposition date deposition_date	2024-03-04
Structure title title	Cryo-EM structure of ADGRG2-Gs complex with NTF nanobody
Keywords keywords	GPCR, MEMBRANE PROTEIN; MEMBRANE 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.

8ykd__assembly_1__model_1

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

Download this curve (.dat)

8ykd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ykd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.23 Å
Rg (electron density)	36.11 Å
Total Rg	36.51 Å
Atom count	9410
Residues	1225
Excluded volume	167710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ykd__assembly_1__model_1`	hexameric （6）	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 (7)

Entity 1 Entity 1 polymer

Description description	Guanine nucleotide-binding protein G(s) subunit alpha
Molecular weight formula_weight	41879.5 kDa
Mutation mutation	G236A,A259D,S262D,L272D,A366S,I372A,V375I
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	9410

MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYELL

Source Source

Source organism organism	Spodoptera
NCBI taxonomy ID ncbi_taxonomy_id	7106
Host organism host_organism	Baculovirus expression vector pFastBac1-HM

Entity 2 Entity 2 polymer

Description description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Molecular weight formula_weight	39418.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Source Source

Source organism organism	Spodoptera
NCBI taxonomy ID ncbi_taxonomy_id	7106
Host organism host_organism	Baculovirus expression vector pFastBac1-HM

Entity 3 Entity 3 polymer

Description description	Guanine nucleotide-binding protein subunit gamma
Molecular weight formula_weight	12104.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MWRELPLGLGELHKDHQASRKLEPELWSVSENPPSTSMASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source Source

Source organism organism	Spodoptera
NCBI taxonomy ID ncbi_taxonomy_id	7106
Host organism host_organism	Baculovirus expression vector pFastBac1-HM

Entity 4 Entity 4 polymer

Description description	Nanobody-35
Molecular weight formula_weight	13885.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQGTQVTVSS

Source Source

Source organism organism	Spodoptera
NCBI taxonomy ID ncbi_taxonomy_id	7106
Host organism host_organism	Baculovirus expression vector pFastBac1-HM

Entity 5 Entity 5 polymer

Description description	Adhesion G-protein coupled receptor G2
Molecular weight formula_weight	98934.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MKTIIALSYIFCLVFADYKDDDDKLKENGNSSLLSPSAESSLVSLIPYSNGTPDAASEVLSTLNKTEKSKITIVKTFNASGVKSQRNICNLSSLCNDSVFFRGEIVFQHDEDHNVTQNQDTANGTFAGVLSLSELKRSELNKTLQTLSETYFIVCATAEAQSTVNCTFTVKLNETMNVCAMMVTFQTVQIRPMEQCCCSPRTPCPSSPEELEKLQCELQDPIVCLADQPHGPPLSSSSKPVVPQATIISHVASDFSLAEPLDHALMTPSTPSLTQESNLPSPQPTIPLASSPATDLPVQSVVVSSLPQTDLSHTLSPVQSSIPSPTTPAPSVPTELVTISTPPGETVVNTSTVSDLEAQVSQMEKALSLGSLEPNLAGEMVNRVSKLLHSPPALLAPLAQRLLKVVDAIGLQLNFSSTTISLTSPSLALAVIRVNASNFNTTTFAAQDPTNLQVSLETPPPENSIGAITLPSSLMNNLPANDVELASRIQFNFFETPALFQDPSLENLTLISYVISSSVTNMTIKNLTRNVTVALKHINPSPDDLTVKCVFWDLGRNGGKGGWSSDGCSVKDKRMNETICTCSALASFGILLDLSRTSLPPSQMMALTFITYIGCGLSSIFLSVTLVTYIAFEKIRRDYPSKILIQLCAALLLLNLIFLLDSWIALYNTRGFCIAVAVFLHYFLLVSFTWMGLEAFHMYLALVKVFNTYIRKYILKFCIVGWGIPAVVVSIVLTISPDNYGIGSYGKFPNGTPDDFCWINSNVVFYITVVGYFCVIFLLNVSMFIVVLVQLCRIKKKKQLGAQRKTSIQDLRSIAGLTFLLGITWGFAFFAWGPVNVTFMYLFAIFNTLQGFFIFIFYCAAKENVRKQWRRYLCCGKLFWFPEKGAILTDTSVKRNDLSIISG

Source Source

Source organism organism	Spodoptera
NCBI taxonomy ID ncbi_taxonomy_id	7106
Host organism host_organism	Baculovirus expression vector pFastBac1-HM

Entity 6 Entity 6 polymer

Description description	ScFv-16
Molecular weight formula_weight	26640.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKGS

Source Source

Source organism organism	Spodoptera
NCBI taxonomy ID ncbi_taxonomy_id	7106
Host organism host_organism	Baculovirus expression vector pFastBac1-HM

Entity 7 Entity 7 non-polymer

Description description	3-BETA-HYDROXY-5-ANDROSTEN-17-ONE
Molecular weight formula_weight	288.4 kDa
Source method src_method	syn
Copy count entity_count	1

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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	2.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	241188

Cryo-EM structure of ADGRG2-Gs complex with NTF nanobody

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

Guanine nucleotide-binding protein G(s) subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-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

Guanine nucleotide-binding protein subunit gamma

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Adhesion G-protein coupled receptor G2

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

8ykd__assembly_1__model_1

8ykd__assembly_1__model_1 | I(q)

8ykd__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 (7)

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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

7. Citations (1)