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- PDB-5vzx: Crystal structure of crenezumab Fab -

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Basic information

Entry
Database: PDB / ID: 5vzx
TitleCrystal structure of crenezumab Fab
Components(Crenezumab Fab ...) x 2
KeywordsIMMUNE SYSTEM / immunoglobulin
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Immunoblobulin light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.501 Å
AuthorsUltsch, M. / Wang, W.
CitationJournal: Sci Rep / Year: 2016
Title: Structure of Crenezumab Complex with Abeta Shows Loss of beta-Hairpin.
Authors: Ultsch, M. / Li, B. / Maurer, T. / Mathieu, M. / Adolfsson, O. / Muhs, A. / Pfeifer, A. / Pihlgren, M. / Bainbridge, T.W. / Reichelt, M. / Ernst, J.A. / Eigenbrot, C. / Fuh, G. / Atwal, J.K. ...Authors: Ultsch, M. / Li, B. / Maurer, T. / Mathieu, M. / Adolfsson, O. / Muhs, A. / Pfeifer, A. / Pihlgren, M. / Bainbridge, T.W. / Reichelt, M. / Ernst, J.A. / Eigenbrot, C. / Fuh, G. / Atwal, J.K. / Watts, R.J. / Wang, W.
History
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 9, 2017ID: 5KMV
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Crenezumab Fab heavy chain
L: Crenezumab Fab light chain
E: Crenezumab Fab heavy chain
I: Crenezumab Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,04819
Polymers94,1254
Non-polymers1,92415
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-168 kcal/mol
Surface area37630 Å2
MethodPISA
2
H: Crenezumab Fab heavy chain
L: Crenezumab Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,07210
Polymers47,0622
Non-polymers1,0108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-79 kcal/mol
Surface area20310 Å2
MethodPISA
3
E: Crenezumab Fab heavy chain
I: Crenezumab Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9769
Polymers47,0622
Non-polymers9147
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-72 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.703, 129.703, 80.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Antibody , 2 types, 4 molecules HELI

#1: Antibody Crenezumab Fab heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 22997.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P0DOX5
#2: Antibody Crenezumab Fab light chain


Mass: 24064.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0KKI6

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Non-polymers , 4 types, 149 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.16 Å3/Da / Density % sol: 70.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.4 M ammonium sulfate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→37.965 Å / Num. obs: 52355 / % possible obs: 99.1 % / Redundancy: 2.8 % / Net I/σ(I): 19.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.501→37.965 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.92
RfactorNum. reflection% reflection
Rfree0.2302 2638 5.09 %
Rwork0.1848 --
obs0.1871 51791 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→37.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6512 0 109 134 6755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066768
X-RAY DIFFRACTIONf_angle_d1.0039202
X-RAY DIFFRACTIONf_dihedral_angle_d14.6722426
X-RAY DIFFRACTIONf_chiral_restr0.0351023
X-RAY DIFFRACTIONf_plane_restr0.0041165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5007-2.54620.32041410.30392516X-RAY DIFFRACTION95
2.5462-2.59520.3021460.28682615X-RAY DIFFRACTION100
2.5952-2.64810.3561250.28662577X-RAY DIFFRACTION100
2.6481-2.70570.37541420.2892609X-RAY DIFFRACTION99
2.7057-2.76860.31161570.27932629X-RAY DIFFRACTION100
2.7686-2.83780.32091390.25562606X-RAY DIFFRACTION100
2.8378-2.91450.3181420.24462589X-RAY DIFFRACTION100
2.9145-3.00030.26651480.24582629X-RAY DIFFRACTION100
3.0003-3.09710.32391440.23052598X-RAY DIFFRACTION99
3.0971-3.20770.25991360.22862596X-RAY DIFFRACTION99
3.2077-3.33610.25841470.23062583X-RAY DIFFRACTION99
3.3361-3.48780.2361380.20052556X-RAY DIFFRACTION98
3.4878-3.67150.23041360.18912568X-RAY DIFFRACTION98
3.6715-3.90130.23391300.17732568X-RAY DIFFRACTION98
3.9013-4.20220.19461370.15982550X-RAY DIFFRACTION97
4.2022-4.62440.18131400.12912577X-RAY DIFFRACTION98
4.6244-5.29210.18661240.13032585X-RAY DIFFRACTION99
5.2921-6.66160.2141360.15882612X-RAY DIFFRACTION99
6.6616-37.96980.17691300.15922590X-RAY DIFFRACTION99
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)
11.9384-0.0273-0.33430.3909-1.06481.26460.2068-0.0426-0.0190.0878-0.19990.1821-0.0522-0.1588-0.00160.56370.1102-0.02320.34-0.01210.6237-10.711653.791653.0164
22.07541.0214-0.16781.6096-0.60860.9282-0.48450.6235-0.0512-0.51370.39230.05560.1134-0.05370.01040.6655-0.07860.04780.4114-0.03070.250415.550133.37123.3535
32.2406-0.9917-0.09672.01580.05970.33990.15060.11710.2455-0.4125-0.2242-0.2051-0.3685-0.0993-0.03470.70940.00520.03690.2510.11270.57118.821763.154845.0329
41.1629-0.45690.15180.8197-0.53030.7268-0.10190.1610.0907-0.0962-0.0174-0.02140.2280.3713-00.6968-0.0166-0.02220.34840.05010.398520.697140.357762.7911
51.89820.82570.02072.01840.17240.60520.0693-0.1669-0.28190.4551-0.2262-0.23830.4153-0.0233-0.05950.7843-0.0072-0.0350.31470.09730.62518.827311.715855.7413
61.64430.3238-0.42210.7655-0.52820.5466-0.0543-0.1485-0.13350.1613-0.0494-0.0054-0.23150.37380.00310.643-0.00310.02420.28210.0390.337720.671234.5737.9558
70.57230.1042-0.07110.01870.08570.1243-0.02180.0214-0.01480.0164-0.0284-0.00320.0239-0.102300.6189-0.0039-0.00830.42120.00280.47232.112239.477349.7717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 1:110 )L1 - 110
2X-RAY DIFFRACTION2( CHAIN I AND RESID 111:214 )I111 - 214
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:114 )H1 - 114
4X-RAY DIFFRACTION4( CHAIN H AND RESID 115:215 )H115 - 215
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:114 )E1 - 114
6X-RAY DIFFRACTION6( CHAIN E AND RESID 115:215 )E115 - 215
7X-RAY DIFFRACTION7( CHAIN I AND RESID 301:305 ) OR ( CHAIN H AND RESID 301:302 ) OR ( CHAIN E AND RESID 301:302 ) OR ( CHAIN L AND RESID 301:306 )I301 - 305
8X-RAY DIFFRACTION7( CHAIN I AND RESID 301:305 ) OR ( CHAIN H AND RESID 301:302 ) OR ( CHAIN E AND RESID 301:302 ) OR ( CHAIN L AND RESID 301:306 )H301 - 302
9X-RAY DIFFRACTION7( CHAIN I AND RESID 301:305 ) OR ( CHAIN H AND RESID 301:302 ) OR ( CHAIN E AND RESID 301:302 ) OR ( CHAIN L AND RESID 301:306 )E301 - 302
10X-RAY DIFFRACTION7( CHAIN I AND RESID 301:305 ) OR ( CHAIN H AND RESID 301:302 ) OR ( CHAIN E AND RESID 301:302 ) OR ( CHAIN L AND RESID 301:306 )L301 - 306

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