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- PDB-6umi: Crystal structure of erenumab Fab-b -

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Basic information

Entry
Database: PDB / ID: 6umi
TitleCrystal structure of erenumab Fab-b
Components
  • erenumab Fab heavy chain, IgG1
  • erenumab Fab light chain, IgG1
KeywordsIMMUNE SYSTEM / Fragment antigen binding
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMohr, C.
CitationJournal: Cell Rep / Year: 2020
Title: Molecular Insight into Recognition of the CGRPR Complex by Migraine Prevention Therapy Aimovig (Erenumab).
Authors: Garces, F. / Mohr, C. / Zhang, L. / Huang, C.S. / Chen, Q. / King, C. / Xu, C. / Wang, Z.
History
DepositionOct 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: erenumab Fab heavy chain, IgG1
L: erenumab Fab light chain, IgG1


Theoretical massNumber of molelcules
Total (without water)48,3112
Polymers48,3112
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-23 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.329, 72.329, 163.762
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-344-

HOH

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Components

#1: Antibody erenumab Fab heavy chain, IgG1


Mass: 25483.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human)
#2: Antibody erenumab Fab light chain, IgG1


Mass: 22827.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M sodium acetate, pH 4.0, 22% PEG6000, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19967 / % possible obs: 99.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.033 / Rrim(I) all: 0.11 / Χ2: 1 / Net I/σ(I): 10.4 / Num. measured all: 215604
Reflection shell

Χ2: 1 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.4911.10.5895.3619350.9290.1830.61799.5
2.49-2.59110.46419470.9570.1450.48699.8
2.59-2.7110.3619540.9690.1130.37899.7
2.7-2.8510.90.25819830.980.0810.27199.8
2.85-3.0210.90.1919800.9870.060.299.8
3.02-3.2610.80.14319760.9920.0450.1599.9
3.26-3.5810.70.11119890.9950.0350.116100
3.58-4.110.50.08919990.9960.0290.09499.7
4.1-5.1710.90.07120550.9970.0230.07599.8
5.17-5010.30.06121490.9980.020.06499.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHASERphasing
MOLREPphasing
REFMAC5.8.0073refinement
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 16.048 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.23
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 955 4.8 %RANDOM
Rwork0.1836 ---
obs0.1854 18974 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.2 Å2 / Biso mean: 46.375 Å2 / Biso min: 24.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 0 138 3447
Biso mean---41.56 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023394
X-RAY DIFFRACTIONr_bond_other_d0.0010.023121
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9494623
X-RAY DIFFRACTIONr_angle_other_deg0.71437224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97724.113124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70715524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4571512
X-RAY DIFFRACTIONr_chiral_restr0.0720.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
LS refinement shellResolution: 2.404→2.466 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 69 -
Rwork0.264 1310 -
all-1379 -
obs--97.52 %
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)
10.4698-0.69130.17952.1428-1.64121.76040.055-0.11220.01460.05660.02670.0566-0.18250.1279-0.08180.1967-0.0838-0.03620.1414-0.02550.0461-26.761-10.82215.345
20.4925-0.3483-0.43871.7808-0.82641.2648-0.03220.0651-0.03960.1115-0.1849-0.191-0.07130.12810.21710.0737-0.0973-0.06850.2370.06270.0922-9.13-14.35913.946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 232
2X-RAY DIFFRACTION2L1 - 213

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