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- PDB-6umh: Crystal structure of erenumab Fab-a -

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Basic information

Entry
Database: PDB / ID: 6umh
TitleCrystal structure of erenumab Fab-a
Components(erenumab Fab ...) x 2
KeywordsIMMUNE SYSTEM / Fragment antigen binding
Function / homology1,3-PROPANDIOL / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: erenumab Fab heavy chain, IgG1
L: erenumab Fab light chain, IgG1
h: erenumab Fab heavy chain, IgG1
l: erenumab Fab light chain, IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,26422
Polymers96,6224
Non-polymers1,64318
Water4,972276
1
H: erenumab Fab heavy chain, IgG1
L: erenumab Fab light chain, IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,22712
Polymers48,3112
Non-polymers91610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-58 kcal/mol
Surface area20420 Å2
MethodPISA
2
h: erenumab Fab heavy chain, IgG1
l: erenumab Fab light chain, IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,03710
Polymers48,3112
Non-polymers7268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-51 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.273, 55.913, 170.086
Angle α, β, γ (deg.)90.000, 110.930, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules HhLl

#1: Antibody erenumab Fab heavy chain, IgG1


Mass: 25483.525 Da / Num. of mol.: 2
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.: 2
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)

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Non-polymers , 4 types, 294 molecules

#3: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium dihydrogen phosphate, 0.1 M Tris, pH 8.5, 50% MPD, 4% 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 6, 2014 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 58318 / % possible obs: 97.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Χ2: 1 / Net I/σ(I): 11.2 / Num. measured all: 400151
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
2.15-2.234.60.5572.3848310.8550.2840.62981.9
2.23-2.325.70.43857060.8970.1990.48396.4
2.32-2.4270.36759340.9570.1470.39599.6
2.42-2.557.20.29158880.9710.1160.31399.8
2.55-2.717.20.21259190.9850.0840.22899.9
2.71-2.927.30.14159220.9930.0560.151100
2.92-3.217.30.0959710.9960.0360.097100
3.21-3.677.30.05859690.9980.0230.063100
3.67-4.637.30.04260230.9990.0170.046100
4.63-307.20.04261550.9990.0170.045100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
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: 2.15→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 11.299 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.176
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 2846 4.9 %RANDOM
Rwork0.1851 ---
obs0.1869 55470 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.59 Å2 / Biso mean: 46.151 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å2-0.17 Å2
2--0.31 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6683 0 96 276 7055
Biso mean--61.41 43.85 -
Num. residues----891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026933
X-RAY DIFFRACTIONr_bond_other_d0.0010.026368
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.969436
X-RAY DIFFRACTIONr_angle_other_deg0.707314742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33824.137249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.748151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1911524
X-RAY DIFFRACTIONr_chiral_restr0.0730.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021521
LS refinement shellResolution: 2.152→2.207 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 168 -
Rwork0.255 3258 -
all-3426 -
obs--79.12 %
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)
10.63980.3160.32631.38211.48053.1486-0.04830.11430.01170.12010.00910.04790.0478-0.12360.03920.0647-0.0299-0.01340.13770.02250.0112-4.732-19.72756.836
20.71130.29970.05820.89460.31192.0738-0.11070.09590.01260.04420.16770.0627-0.16910.1896-0.0570.0796-0.0558-0.00060.2050.02510.01328.298-11.92752.067
30.6099-0.47410.45691.2776-1.32772.70260.00850.2064-0.05440.0581-0.1247-0.0192-0.1868-0.12040.11620.0656-0.0469-0.01920.3853-0.04210.01733.1012.04114.497
40.564-0.4741-0.09420.4853-0.3083.05840.0870.165-0.0046-0.0612-0.01970.0450.0449-0.7885-0.06720.0769-0.0871-0.00160.54280.01460.067518.502-2.58319.61
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 232
2X-RAY DIFFRACTION2L2 - 213
3X-RAY DIFFRACTION3h1 - 232
4X-RAY DIFFRACTION4l2 - 213

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