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- PDB-6knm: Apelin receptor in complex with single domain antibody -

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Basic information

Entry
Database: PDB / ID: 6knm
TitleApelin receptor in complex with single domain antibody
Components
  • Apelin receptor,Rubredoxin,Apelin receptor
  • Single domain antibody JN241
KeywordsMEMBRANE PROTEIN / GPCR / Single-domain antibody / Antagonist / Agonist
Function / homology
Function and homology information


apelin receptor activity / apelin receptor signaling pathway / regulation of gap junction assembly / positive regulation of inhibitory G protein-coupled receptor phosphorylation / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / alkane catabolic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...apelin receptor activity / apelin receptor signaling pathway / regulation of gap junction assembly / positive regulation of inhibitory G protein-coupled receptor phosphorylation / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / alkane catabolic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endocardial cushion formation / C-C chemokine receptor activity / coronary vasculature development / C-C chemokine binding / adult heart development / vasculature development / negative regulation of cAMP-mediated signaling / aorta development / ventricular septum morphogenesis / blood vessel development / heart looping / vasculogenesis / gastrulation / Peptide ligand-binding receptors / neurogenesis / cell chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / G protein-coupled receptor activity / calcium-mediated signaling / brain development / positive regulation of angiogenesis / signaling receptor activity / heart development / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / regulation of gene expression / angiogenesis / electron transfer activity / iron ion binding / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / plasma membrane
Similarity search - Function
Apelin receptor / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Apelin receptor / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Rubredoxin / Apelin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMa, Y.B. / Ding, Y. / Song, X. / Ma, X. / Li, X. / Zhang, N. / Song, Y. / Sun, Y. / Shen, Y. / Zhong, W. ...Ma, Y.B. / Ding, Y. / Song, X. / Ma, X. / Li, X. / Zhang, N. / Song, Y. / Sun, Y. / Shen, Y. / Zhong, W. / Hu, L.A. / Ma, Y.L. / Zhang, M.Y.
CitationJournal: Sci Adv / Year: 2020
Title: Structure-guided discovery of a single-domain antibody agonist against human apelin receptor.
Authors: Ma, Y. / Ding, Y. / Song, X. / Ma, X. / Li, X. / Zhang, N. / Song, Y. / Sun, Y. / Shen, Y. / Zhong, W. / Hu, L.A. / Ma, Y. / Zhang, M.Y.
History
DepositionAug 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Advisory / Database references
Category: citation / citation_author / pdbx_database_PDB_obs_spr
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Apelin receptor,Rubredoxin,Apelin receptor
A: Single domain antibody JN241
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2753
Polymers60,2102
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-15 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.780, 48.390, 350.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apelin receptor,Rubredoxin,Apelin receptor / Angiotensin receptor-like 1 / G-protein coupled receptor APJ / G-protein coupled receptor HG11 / Rd ...Angiotensin receptor-like 1 / G-protein coupled receptor APJ / G-protein coupled receptor HG11 / Rd / Angiotensin receptor-like 1 / G-protein coupled receptor APJ / G-protein coupled receptor HG11


Mass: 46443.621 Da / Num. of mol.: 1
Mutation: V117A, T177N,W261K, C325L, C326M,V117A, T177N,W261K, C325L, C326M,V117A, T177N,W261K, C325L, C326M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: APLNR, AGTRL1, APJ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35414, UniProt: P00268
#2: Antibody Single domain antibody JN241


Mass: 13766.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 65.34 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM MES pH 6.1, 26% PEG500 DME, 125 mM MgCl2, 100 mM NaCl

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→46.641 Å / Num. obs: 12402 / % possible obs: 92.5 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.2-3.281.8440.2811.8610869495890.940.36962.1
3.28-3.371.9840.2821.7513919337010.9230.35275.1
3.37-3.472.150.2551.9118349598530.9480.31188.9
3.47-3.583.110.322.3324978378030.8780.37695.9
3.58-3.73.430.2812.630058958760.9510.32297.9
3.7-3.833.5580.2453.0128298147950.9760.27897.7
3.83-3.973.6960.2283.5829468257970.9760.25796.6
3.97-4.133.5160.2213.827397967790.9650.25297.9
4.13-4.323.890.2134.9328247427260.9780.23997.8
4.32-4.533.5880.2035.0325267247040.9650.23197.2
4.53-4.773.6490.1735.4425036946860.9790.19698.8
4.77-5.063.5530.1725.7422996736470.9730.19696.1
5.06-5.413.4780.1735.7821016166040.9610.19998.1
5.41-5.843.7250.1666.1120715665560.9640.19198.2
5.84-6.43.6310.1586.2519685555420.9760.1897.7
6.4-7.163.4120.1356.7916144954730.9840.15595.6
7.16-8.263.2680.1277.3814254474360.9640.14997.5
8.26-10.123.4620.1118.4312813783700.9780.1397.9
10.12-14.312.9580.1027.948553112890.9940.12392.9
14.31-46.6412.8350.0817.844991961760.9960.189.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NC2, 5VBL

4nc2

5vbl


Resolution: 3.2→46.641 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.86 / Phase error: 34.67
RfactorNum. reflection% reflection
Rfree0.3051 619 5.01 %
Rwork0.2575 --
obs0.2598 12361 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 192.15 Å2 / Biso mean: 95.5703 Å2 / Biso min: 67.94 Å2
Refinement stepCycle: final / Resolution: 3.2→46.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 422 0 4168
Biso mean--94.76 --
Num. residues----426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2004-3.52240.43921250.379238177
3.5224-4.03180.38761610.2911304197
4.0318-5.07870.28141620.2244308497
5.0787-46.640.25761710.237323697
Refinement TLS params.Method: refined / Origin x: -2.6352 Å / Origin y: 14.0224 Å / Origin z: -43.999 Å
111213212223313233
T0.7684 Å20.0264 Å20.0127 Å2-0.7122 Å20.0127 Å2--0.6866 Å2
L0.0748 °2-0.0491 °20.02 °2-0.0821 °20.0099 °2--0.0197 °2
S-0.1 Å °-0.1242 Å °-0.0238 Å °-0.2154 Å °-0.0286 Å °0.0074 Å °-0.0835 Å °0.0799 Å °-0.0417 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB18 - 327
2X-RAY DIFFRACTION1allB1001 - 1054
3X-RAY DIFFRACTION1allA1 - 129
4X-RAY DIFFRACTION1allD1

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