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- PDB-4nwu: Crystal structure of APE1551, an anti-human NGF Fab with a nine a... -

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Basic information

Entry
Database: PDB / ID: 4nwu
TitleCrystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in CDR H1
Components
  • APE1551 Ab Fab heavy chain
  • APE1551 Ab Fab light chain
KeywordsIMMUNE SYSTEM / beta-sandwich / human beta nerve growth factor
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsVerdino, P. / Stanfield, R.L. / Wilson, I.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies.
Authors: Bowers, P.M. / Verdino, P. / Wang, Z. / da Silva Correia, J. / Chhoa, M. / Macondray, G. / Do, M. / Neben, T.Y. / Horlick, R.A. / Stanfield, R.L. / Wilson, I.A. / King, D.J.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jun 2, 2021Group: Database references / Refinement description / Source and taxonomy
Category: entity_src_gen / software / struct_ref_seq
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _software.name / _struct_ref_seq.db_align_end
Revision 1.5Apr 3, 2024Group: 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
H: APE1551 Ab Fab heavy chain
L: APE1551 Ab Fab light chain


Theoretical massNumber of molelcules
Total (without water)50,3092
Polymers50,3092
Non-polymers00
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-27 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.053, 66.256, 63.884
Angle α, β, γ (deg.)90.00, 108.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-322-

HOH

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Components

#1: Antibody APE1551 Ab Fab heavy chain


Mass: 25965.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Antibody APE1551 Ab Fab light chain


Mass: 24342.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 6000, 0.1 M Citric acid pH6.0-7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: PILATUS 6M-PAD / Detector: PIXEL / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→45.58 Å / Num. obs: 64694 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3210 / % possible all: 96.3

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APE1531 Fab

Resolution: 1.602→45.58 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.701 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19767 3280 5.1 %RANDOM
Rwork0.16628 ---
obs0.16787 61414 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.558 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0 Å20.01 Å2
2--3.46 Å2-0 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.602→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 0 434 3884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023882
X-RAY DIFFRACTIONr_bond_other_d0.0010.023552
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.955351
X-RAY DIFFRACTIONr_angle_other_deg0.8973.0018277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80324.34159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48815643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1321517
X-RAY DIFFRACTIONr_chiral_restr0.1290.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214572
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02905
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 248 -
Rwork0.259 4453 -
obs--96.33 %
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)
11.30860.72420.62372.37291.5522.81220.0412-0.1192-0.23530.0963-0.12670.00580.29240.05050.08550.24640.01610.03390.20610.01850.246237.402119.561128.664
22.3121-0.1494-2.17270.62350.1183.89090.04050.06190.0074-0.06850.03740.0360.0792-0.1116-0.0780.2487-0.0319-0.00880.0784-0.01290.23215.770219.057229.7301
33.72990.4762-1.54481.1484-0.51632.7446-0.1257-0.0051-0.03010.05050.06620.08950.08920.01820.05940.1788-0.0077-0.00540.0069-0.00570.168931.28127.412360.6045
42.70810.96461.32982.12591.34021.9741-0.0765-0.13740.1287-0.0528-0.00650.0427-0.0927-0.18950.08290.19930.00460.00570.03250.00740.184319.445638.491962.5482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 113
2X-RAY DIFFRACTION2L1 - 108
3X-RAY DIFFRACTION3H114 - 230
4X-RAY DIFFRACTION4L109 - 214

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