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- PDB-4kte: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE1... -

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Basic information

Entry
Database: PDB / ID: 4kte
TitleFab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate
Components
  • GE148 Heavy Chain Fab
  • GE148 Light Chain Fab
KeywordsIMMUNE SYSTEM / Antibody Affinity / Antibody Specificity / Vaccine Elicited Antibodies / Fab fragment / AIDS Vaccines
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPoulsen, C. / Tran, K. / Stanfield, R. / Wyatt, R.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign.
Authors: Tran, K. / Poulsen, C. / Guenaga, J. / de Val Alda, N. / Wilson, R. / Sundling, C. / Li, Y. / Stanfield, R.L. / Wilson, I.A. / Ward, A.B. / Karlsson Hedestam, G.B. / Wyatt, R.T.
History
DepositionMay 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: GE148 Heavy Chain Fab
L: GE148 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8316
Polymers48,4512
Non-polymers3804
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-67 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.710, 72.040, 175.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody GE148 Heavy Chain Fab


Mass: 24822.838 Da / Num. of mol.: 1 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo sapiens (human)
#2: Antibody GE148 Light Chain Fab


Mass: 23628.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.17M NH4SO4, 25.5%(w/v) PEG4000, 15%(v/v) Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 51295 / Num. obs: 51192 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.458 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.09
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.850.4974.062899839821100
1.85-1.90.3795.292596235661100
1.9-20.2647.444471661281100
2-2.40.14713.0311396615601199.9
2.4-2.80.08121.89580517985199.9
2.8-40.03939.93643519046199.7
4-80.02852.92292654257199.4
8-150.02555.163560566199.5
15-200.02451.3834961198.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.94 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8897 / SU ML: 0.4 / σ(F): 2 / Phase error: 17.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 2560 5 %Random
Rwork0.1647 ---
obs0.1662 51191 99.85 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.208 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 80.58 Å2 / Biso mean: 25.9475 Å2 / Biso min: 8.08 Å2
Baniso -1Baniso -2Baniso -3
1--2.6899 Å20 Å2-0 Å2
2--5.0094 Å20 Å2
3----2.3195 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 21 496 3776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063366
X-RAY DIFFRACTIONf_angle_d1.1544593
X-RAY DIFFRACTIONf_chiral_restr0.079521
X-RAY DIFFRACTIONf_plane_restr0.005579
X-RAY DIFFRACTIONf_dihedral_angle_d12.91181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83460.20771390.188626472786100
1.8346-1.8720.24111400.194826622802100
1.872-1.91270.24521400.183526572797100
1.9127-1.95710.23071420.173226922834100
1.9571-2.0060.21591400.160526622802100
2.006-2.06020.20171400.159426612801100
2.0602-2.12080.24571410.163126822823100
2.1208-2.18910.19861410.160126712812100
2.1891-2.26730.19261420.159226982840100
2.2673-2.35790.18251400.16426602800100
2.3579-2.4650.18821420.16526922834100
2.465-2.59470.20151410.168526952836100
2.5947-2.75690.23261420.177926952837100
2.7569-2.96920.221430.168627202863100
2.9692-3.26680.18841450.169827492894100
3.2668-3.73680.18241430.15712713285699
3.7368-4.69780.14961460.137227772923100
4.6978-19.94140.17691530.18112898305199
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)
14.5778-1.9611-0.94431.6948-0.08563.2957-0.00540.27260.0598-0.0466-0.0118-0.02190.08320.0873-0.01470.0883-0.016700.0742-0.02210.069912.8206-29.9237-24.8716
23.1255-0.1437-0.35142.18690.29752.4236-0.1767-0.2075-0.12690.04940.0975-0.11110.1480.19890.08050.06650.01130.00250.0896-0.00450.066518.5987-28.0906-13.8152
36.3139-1.3355-0.88122.1924-0.31082.423-0.22960.0012-0.43570.05050.13910.03010.23790.02010.10020.0941-0.02550.01930.0852-0.0340.094512.8015-32.584-19.4014
40.16780.17020.78170.75640.53143.7452-0.25770.626-0.06010.03840.2693-0.1749-0.13450.59290.03570.0952-0.0086-0.0080.1016-0.02140.132322.8479-22.4739-17.039
58.57011.72396.51180.95831.24294.95130.04890.051-0.05870.01080.06350.07580.19330.0912-0.1230.10340.0202-0.01990.1237-0.02460.134828.6799-19.2145-10.3058
61.0265-1.06150.70441.6399-0.34294.2257-0.07320.04020.072-0.03680.08580.12150.1035-0.2409-0.00490.0911-0.03580.00540.09190.00780.10822.3843-25.2356-27.962
71.394-0.0505-0.2252.2318-0.62462.28210.05560.03570.2493-0.15160.1866-0.2872-0.2727-0.0121-0.16510.1244-0.03250.04680.073-0.02390.16243.771-13.1462-41.744
83.43672.1746-2.71825.6497-4.6316.73490.06190.21370.166-0.70820.0601-0.11980.40620.0719-0.10430.27070.00510.03770.1036-0.02410.13646.6159-19.5003-47.8529
93.00630.08030.4412.3874-0.03442.3773-0.14080.02580.3264-0.11930.03890.0359-0.27590.13880.0710.1299-0.0315-0.04370.11150.0070.128421.9744-6.6387-11.5552
101.78470.39640.78313.89190.95563.65010.0083-0.0070.00270.01120.04880.2299-0.2556-0.0923-0.04150.1246-0.0001-0.00330.06840.01610.1151-5.5086-2.1702-39.7597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 2:25 )H2 - 25
2X-RAY DIFFRACTION2( CHAIN H AND RESID 26:74 )H26 - 74
3X-RAY DIFFRACTION3( CHAIN H AND RESID 75:92 )H75 - 92
4X-RAY DIFFRACTION4( CHAIN H AND RESID 93:104 )H93 - 104
5X-RAY DIFFRACTION5( CHAIN H AND RESID 105:116 )H105 - 116
6X-RAY DIFFRACTION6( CHAIN H AND RESID 117:126 )H117 - 126
7X-RAY DIFFRACTION7( CHAIN H AND RESID 134:201 )H134 - 201
8X-RAY DIFFRACTION8( CHAIN H AND RESID 202:213 )H202 - 213
9X-RAY DIFFRACTION9( CHAIN L AND RESID 2:115 )L2 - 115
10X-RAY DIFFRACTION10( CHAIN L AND RESID 116:208 )L116 - 208

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