[English] 日本語
Yorodumi
- PDB-4lf3: Inhibitory Mechanism of an Allosteric Antibody Targeting the Gluc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lf3
TitleInhibitory Mechanism of an Allosteric Antibody Targeting the Glucagon Receptor
Components
  • Fab heavy chain
  • Fab light chain
  • Glucagon receptor
KeywordsIMMUNE SYSTEM / Fab fragment / GCGR
Function / homology
Function and homology information


regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / peptide hormone binding / response to nutrient / cellular response to glucagon stimulus / guanyl-nucleotide exchange factor activity / cellular response to starvation / generation of precursor metabolites and energy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway ...regulation of glycogen metabolic process / glucagon receptor activity / response to starvation / peptide hormone binding / response to nutrient / cellular response to glucagon stimulus / guanyl-nucleotide exchange factor activity / cellular response to starvation / generation of precursor metabolites and energy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of blood pressure / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Glucagon-type ligand receptors / glucose homeostasis / G alpha (s) signalling events / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of gene expression / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, glucagon receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain ...GPCR, family 2, glucagon receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.735 Å
AuthorsMurray, J.M. / Mukund, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Inhibitory mechanism of an allosteric antibody targeting the glucagon receptor.
Authors: Mukund, S. / Shang, Y. / Clarke, H.J. / Madjidi, A. / Corn, J.E. / Kates, L. / Kolumam, G. / Chiang, V. / Luis, E. / Murray, J. / Zhang, Y. / Hotzel, I. / Koth, C.M. / Allan, B.B.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Database references
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab heavy chain
B: Fab light chain
C: Glucagon receptor
D: Fab heavy chain
E: Fab light chain
F: Glucagon receptor


Theoretical massNumber of molelcules
Total (without water)119,2316
Polymers119,2316
Non-polymers00
Water1,838102
1
A: Fab heavy chain
B: Fab light chain
C: Glucagon receptor


Theoretical massNumber of molelcules
Total (without water)59,6163
Polymers59,6163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fab heavy chain
E: Fab light chain
F: Glucagon receptor


Theoretical massNumber of molelcules
Total (without water)59,6163
Polymers59,6163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.928, 62.777, 116.432
Angle α, β, γ (deg.)90.000, 106.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.858691, -0.005308, 0.512467), (-0.004429, -0.999986, -0.002935), (0.512475, 0.000251, -0.858702)-14.9113, -28.5179, 56.242802
2given(0.859228, -0.001551, 0.51159), (-0.008335, -0.999905, 0.010968), (0.511524, -0.013688, -0.85916)-14.7913, -29.1805, 55.934299
3given(0.855034, 0.011903, 0.518435), (0.005818, -0.999894, 0.013362), (0.518539, -0.008408, -0.855012)-14.8813, -29.0529, 55.9174

-
Components

#1: Antibody Fab heavy chain


Mass: 23263.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anti GCGR mAb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Antibody Fab light chain


Mass: 25000.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anti GCGR mAb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Protein Glucagon receptor / GL-R


Mass: 11350.929 Da / Num. of mol.: 2 / Fragment: GCGR ECD (UNP residues 29-123) / Mutation: G40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCGR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P47871
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 0.2 M NaCl, PEG3350, pH 8.5, vapor diffusion, hanging drop, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: ADSC / Detector: CCD / Date: Apr 25, 2011
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.735→55.95 Å / Num. all: 35933 / Num. obs: 35933 / % possible obs: 92.6 % / Redundancy: 2.9 % / Rsym value: 0.066 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.735-2.882.60.3672.11366251740.36792.4
2.88-3.0630.2383.31517051290.23895.8
3.06-3.2730.1594.91427447710.15995.3
3.27-3.5330.09681299443980.09694
3.53-3.872.90.07110.81137439730.07192.8
3.87-4.322.70.04715.7952434850.04789.6
4.32-4.993.10.03420.9969631640.03491.2
4.99-6.123.10.03418.5826026780.03490.3
6.12-8.652.90.03121.5573820000.03188.4
8.65-55.953.20.02227.1372611610.02288.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.76
Highest resolutionLowest resolution
Rotation2.73 Å55.95 Å
Translation2.73 Å55.95 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ERS

4ers


Resolution: 2.735→55.95 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.02 / Cross valid method: Random / σ(F): 1.35 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 1788 4.98 %
Rwork0.2088 --
obs0.2116 35910 92.16 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.147 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 172.47 Å2 / Biso mean: 52.4367 Å2 / Biso min: 4.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.0451 Å2-0 Å2-4.5211 Å2
2---5.59 Å20 Å2
3---3.5449 Å2
Refinement stepCycle: LAST / Resolution: 2.735→55.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8368 0 0 102 8470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018586
X-RAY DIFFRACTIONf_angle_d1.53811655
X-RAY DIFFRACTIONf_chiral_restr0.0921264
X-RAY DIFFRACTIONf_plane_restr0.0091499
X-RAY DIFFRACTIONf_dihedral_angle_d16.2343077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.735-2.80870.44071440.35742520266490
2.8087-2.89140.4351250.33472673279894
2.8914-2.98470.31831450.26052705285095
2.9847-3.09130.29561310.23422683281496
3.0913-3.21510.31061330.22112711284495
3.2151-3.36140.27261500.22122647279795
3.3614-3.53860.27291390.22052662280193
3.5386-3.76030.25231490.21622615276493
3.7603-4.05050.25531260.19512556268289
4.0505-4.4580.20771380.16532589272790
4.458-5.10270.21761370.15692595273291
5.1027-6.42740.24591340.19612582271690
6.4274-55.96130.22931370.19182584272187
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05340.065-0.12571.02160.16020.6468-0.03760.05110.26230.0425-0.0506-0.2421-0.25020.08290.02610.3051-0.0619-0.06050.0860.04520.143210.314710.266311.8661
21.10730.07470.20850.9250.20740.609-0.0042-0.12650.09290.26170.072-0.1445-0.22510.01830.0260.49920.0244-0.09840.0943-0.1080.20578.44668.003818.382
31.9011-0.11990.35880.2652-0.46040.8102-0.25090.1788-0.16470.03220.3182-0.8864-0.0404-0.18350.07870.4451-0.1632-0.16190.3901-0.08280.493731.78869.871718.9562
40.7042-0.51920.02962.75750.87391.3294-0.10630.2459-0.0145-0.42550.0633-0.4284-0.05750.4930.13890.4874-0.21640.14680.6128-0.13290.789442.8976-7.361112.4502
51.2945-0.34090.00352.207-0.12071.3025-0.16110.3762-0.399-0.5210.1099-0.90570.01990.24040.04580.5676-0.32850.13770.6467-0.09620.647943.7195-5.53519.4414
62.1899-0.1097-0.11461.0162-0.24341.34850.3054-0.2497-0.0146-0.07330.0331-0.33780.0556-0.14570.04940.3823-0.0985-0.02240.10730.06990.14758.6462-17.909717.7933
70.94270.16010.95391.5983-0.07380.99660.0871-0.06960.0381-0.07820.05030.0504-0.1087-0.14150.03070.2841-0.04140.03550.03050.0633-0.09311.4929-12.310312.9121
80.8030.21970.49230.7509-0.07180.99830.0323-0.2191-0.11380.23140.101-0.4521-0.07130.1992-0.09270.2445-0.024-0.08760.1684-0.05350.251228.9064-11.996621.1241
92.73411.14111.03321.9448-0.4461.46080.0943-0.75-0.25070.682-0.37760.37070.2302-0.54650.00590.4872-0.10940.19630.66170.18570.4526-29.9805-4.436714.6247
102.29680.53450.97731.527-0.12863.30390.0494-0.175-0.4258-0.12880.03610.4873-0.0266-0.4739-0.0880.28510.01360.04460.18420.02790.3045-23.861-2.00010.7323
111.18-0.09840.24490.9066-0.26420.6180.0126-0.0528-0.30080.1306-0.0116-0.23320.111-0.07560.01160.1138-0.02430.05690.12040.00980.1888-1.2475-38.972751.1355
120.871-0.52630.40130.6339-0.13290.52660.10060.0971-0.2143-0.1324-0.063-0.12750.10730.08940.01550.08310.01840.05520.0298-0.03860.21180.5356-36.781844.5604
131.6777-0.3629-0.45230.2085-0.14660.5784-0.0582-0.1347-0.0794-0.03180.1081-0.5957-0.0334-0.1599-0.33220.11910.07240.07290.21850.09070.426320.7784-39.072556.0265
140.0033-0.07260.03811.2231-0.56290.3749-0.0263-0.16130.00350.1903-0.1883-0.6565-0.2210.06830.2540.16710.0978-0.15880.24110.07560.470727.0539-21.45467.0659
151.29040.10260.32381.87830.02241.0755-0.0621-0.20470.05010.4804-0.0326-0.3604-0.09250.1186-0.00150.28690.144-0.18020.37040.07760.436326.2408-23.269870.072
160.99770.4970.44720.9268-0.02591.90840.09240.08930.10340.02820.1259-0.3751-0.04260.0137-0.05720.06440.00570.05670.11640.11050.17280.5641-10.832245.1964
170.8381-0.1714-0.45551.2809-0.31810.90560.19070.18630.175-0.2225-0.03250.1558-0.0632-0.04710.11880.14980.05690.07990.18670.06650.1791-6.4382-17.355839.6304
181.629-0.2752-0.40832.13620.45250.2742-0.03630.01840.05610.0026-0.0111-0.0116-0.0159-0.1435-0.01240.08020.01080.07540.10130.07370.1371-8.6207-16.057447.7578
191.26460.5874-0.02850.96530.31670.4481-0.00840.22870.0118-0.08460.0194-0.18410.03040.1342-0.05440.10840.04440.04750.1580.03210.11043.4082-21.143547.9345
201.7145-0.2167-0.32911.83010.09880.8618-0.07920.03970.0598-0.1087-0.0522-0.53670.09580.18740.04180.04720.03690.13210.2201-0.01870.483228.6937-14.315755.0711
212.9375-0.52570.00533.99880.26111.41740.46480.72520.1045-1.14790.0464-0.2652-0.5387-0.25280.13160.5938-0.0189-0.22370.87230.20310.4762-34.7314-24.025928.1382
222.38540.0627-0.87121.4012-0.40491.7302-0.18670.3930.2711-0.09660.0890.5506-0.02-0.44440.06450.1832-0.0068-0.030.20730.00940.3063-36.1744-26.800442.8006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:38)A1 - 38
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 39:102)A39 - 102
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 103:113)A103 - 113
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 114:150)A114 - 150
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 151:214)A151 - 214
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 215:231)B215 - 231
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 232:313)B232 - 313
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 314:445)B314 - 445
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 29:47)C29 - 47
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 48:123)C48 - 123
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 1:38)D1 - 38
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 39:102)D39 - 102
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 103:113)D103 - 113
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 114:150)D114 - 150
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 151:214)D151 - 214
16X-RAY DIFFRACTION16CHAIN E AND (RESSEQ 215:231)E215 - 231
17X-RAY DIFFRACTION17CHAIN E AND (RESSEQ 232:253)E232 - 253
18X-RAY DIFFRACTION18CHAIN E AND (RESSEQ 254:313)E254 - 313
19X-RAY DIFFRACTION19CHAIN E AND (RESSEQ 314:363)E314 - 363
20X-RAY DIFFRACTION20CHAIN E AND (RESSEQ 364:445)E364 - 445
21X-RAY DIFFRACTION21CHAIN F AND (RESSEQ 30:47)F30 - 47
22X-RAY DIFFRACTION22CHAIN F AND (RESSEQ 48:123)F48 - 123

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more