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- PDB-4jpi: Crystal structure of a putative VRC01 germline precursor Fab -

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Basic information

Entry
Database: PDB / ID: 4jpi
TitleCrystal structure of a putative VRC01 germline precursor Fab
Components
  • Putative VRC01 germline Fab heavy chain
  • Putative VRC01 germline Fab light chain
KeywordsIMMUNE SYSTEM / anti-HIV-1 / gp120 / CD4 binding site-targeting / VRC01 broadly neutralizing antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJulien, J.-P. / Diwanji, D.C. / Jardine, J. / Schief, W.R. / Wilson, I.A.
CitationJournal: Science / Year: 2013
Title: Rational HIV immunogen design to target specific germline B cell receptors.
Authors: Jardine, J. / Julien, J.P. / Menis, S. / Ota, T. / Kalyuzhniy, O. / McGuire, A. / Sok, D. / Huang, P.S. / MacPherson, S. / Jones, M. / Nieusma, T. / Mathison, J. / Baker, D. / Ward, A.B. / ...Authors: Jardine, J. / Julien, J.P. / Menis, S. / Ota, T. / Kalyuzhniy, O. / McGuire, A. / Sok, D. / Huang, P.S. / MacPherson, S. / Jones, M. / Nieusma, T. / Mathison, J. / Baker, D. / Ward, A.B. / Burton, D.R. / Stamatatos, L. / Nemazee, D. / Wilson, I.A. / Schief, W.R.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 18, 2013Group: Source and taxonomy
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
H: Putative VRC01 germline Fab heavy chain
L: Putative VRC01 germline Fab light chain
A: Putative VRC01 germline Fab heavy chain
B: Putative VRC01 germline Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6479
Polymers99,1864
Non-polymers4605
Water6,972387
1
H: Putative VRC01 germline Fab heavy chain
L: Putative VRC01 germline Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8695
Polymers49,5932
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-25 kcal/mol
Surface area19180 Å2
MethodPISA
2
A: Putative VRC01 germline Fab heavy chain
B: Putative VRC01 germline Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7774
Polymers49,5932
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-20 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.440, 172.440, 92.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Antibody Putative VRC01 germline Fab heavy chain


Mass: 26557.623 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)
#2: Antibody Putative VRC01 germline Fab light chain


Mass: 23035.514 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)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% w/v PEG3350, 0.2 M lithium citrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→86.22 Å / Num. all: 59819 / Num. obs: 59809 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 30.03 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.521 / % possible all: 100

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGB CHAINS H AND L

3ngb


Resolution: 2.1→44.149 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 0.1 / Phase error: 22.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2914 4.99 %RANDOM
Rwork0.1747 55486 --
obs0.1766 58400 97.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.62 Å2 / Biso mean: 42.283 Å2 / Biso min: 14.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 30 387 6905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076676
X-RAY DIFFRACTIONf_angle_d1.1059058
X-RAY DIFFRACTIONf_chiral_restr0.0781006
X-RAY DIFFRACTIONf_plane_restr0.0051156
X-RAY DIFFRACTIONf_dihedral_angle_d14.5632385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13450.29811310.25242551268294
2.1345-2.17130.30651360.24892573270995
2.1713-2.21070.25861290.22782548267794
2.2107-2.25330.27371390.23332565270496
2.2533-2.29930.28631420.23052596273896
2.2993-2.34920.22861320.22692595272796
2.3492-2.40390.32511380.23032612275097
2.4039-2.4640.30681350.22982598273396
2.464-2.53060.28061410.21962649279097
2.5306-2.60510.29461450.21852655280098
2.6051-2.68910.2641390.20672635277498
2.6891-2.78520.23711400.20252653279398
2.7852-2.89670.24591400.19512664280499
2.8967-3.02860.22851400.17952673281399
3.0286-3.18820.21811390.17282703284299
3.1882-3.38790.19271370.163126752812100
3.3879-3.64930.18391430.145227272870100
3.6493-4.01630.20281410.145227132854100
4.0163-4.5970.1571440.124226892833100
4.597-5.78970.15741420.138427112853100
5.7897-44.1590.17531410.166827012842100
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)
14.0796-4.29530.09716.5060.48941.5240.008-0.2693-0.2070.34250.08030.27860.072-0.0837-0.09820.2015-0.06040.01190.25320.03330.2094-1.680924.9737-22.8747
25.1508-1.03540.85342.3983-0.1481.49670.03950.21-0.2683-0.1943-0.060.21440.0986-0.10220.02270.2458-0.0325-0.01590.20680.0130.1907-0.770624.4974-32.735
39.1901-6.13660.36338.28791.79021.64160.43380.5523-0.7986-0.5108-0.35770.44840.1169-0.1025-0.07150.283-0.0088-0.05690.2420.02720.25672.085816.2498-29.7998
42.040.6384-0.54053.87510.28122.5504-0.01290.2060.1210.09560.01960.285-0.2767-0.1702-0.01630.1722-0.0071-0.01340.22650.00020.18173.638231.2242-27.7622
54.67951.05434.07563.4522.07036.28020.2894-0.3337-0.46680.3103-0.07480.08460.3884-0.3085-0.22950.2657-0.0173-0.01190.240.0290.27326.603715.2626-8.2491
65.57053.00543.09615.01183.69957.1538-0.04170.070.457-0.1085-0.1959-0.1536-0.09220.22160.20510.18-0.00080.01670.29840.08740.340424.272939.5865-33.7265
74.7288-0.53831.84484.6845-3.4777.48390.04960.56640.1722-0.5262-0.0076-0.02720.24940.071-0.06710.2015-0.0319-0.00570.23190.05350.229313.540140.1115-38.2254
83.6838-0.6117-1.01384.92760.06922.48910.0622-0.03070.3660.0803-0.0801-0.2881-0.19370.315-0.00560.171-0.015-0.01320.22730.01230.207413.229943.8647-29.8125
93.1922.63764.21077.82282.69676.0020.3227-0.50290.07390.4182-0.3562-0.49840.1309-0.1380.06710.2102-0.04530.0480.36210.03670.245316.375437.7237-30.7637
107.9949-4.02086.01262.0314-3.0844.3343-0.3633-0.0365-0.04990.26350.33160.1093-0.093-0.181-0.04910.2163-0.0008-0.01370.273-0.00030.230133.627135.3436-23.5177
115.85884.716-0.33299.2282-3.47173.43430.2837-0.4371-0.58760.676-0.209-0.42210.10020.0754-0.06630.38890.0414-0.10580.3201-0.00130.297336.4258.2014-9.9201
121.2846-0.53190.37266.5748-0.51591.70770.07070.2745-0.3411-0.31210.0083-0.3220.2830.1291-0.0930.25640.0013-0.02450.264-0.05190.297438.20416.2263-22.0586
132.30731.27520.33183.2964-1.63042.50820.0119-0.0866-0.19590.32310.0428-0.60290.09980.04450.00760.31880.0081-0.06070.2875-0.05130.267840.026716.0511-18.3339
147.9046-1.32672.93952.1701-1.13563.3027-0.01930.5076-0.0646-0.53410.0607-0.27140.34960.2344-0.08380.4146-0.01460.07550.1988-0.04080.269631.09190.3958-54.9036
152.7224-1.27271.83677.9065-3.3944.3951-0.0708-0.17940.0072-0.12370.0936-0.0199-0.0462-0.31340.0070.2841-0.01580.02950.27540.0050.21224.41933.5264-45.4237
162.1743-0.54531.68191.8937-0.71413.0799-0.0916-0.0286-0.1624-0.31450.150.02280.1914-0.0674-0.10650.3103-0.03370.060.2210.00340.216425.24663.3784-53.7413
174.20891.3126-1.61143.2927-2.17624.91390.12530.2842-0.0617-0.2812-0.01560.2311-0.0376-0.0597-0.12320.4003-0.0033-0.0090.2572-0.04580.248416.447323.5361-78.5945
184.50922.273-3.35234.9558-2.62926.3657-0.1123-0.18630.11270.1129-0.11310.0541-0.55240.35080.2310.35340.014-0.05850.2254-0.04030.263427.924930.6022-45.2835
194.0662-0.6009-0.56746.1790.55285.6453-0.1794-0.06630.1081-0.13360.1118-0.1378-0.17990.10020.01860.1693-0.0026-0.01810.1761-0.00550.191831.839320.7409-42.9794
204.8271.6272-1.27646.6268-2.53126.4403-0.2096-0.0719-0.03490.06320.1093-0.5728-0.31070.51890.09920.2144-0.0284-0.01360.218-0.04040.241938.847624.1982-41.0433
214.93032.29510.10328.6956-4.61246.9522-0.2043-0.19870.008-0.18260.01370.0072-0.12080.28470.17730.35130.0190.05610.2654-0.06820.221230.718822.6325-46.7822
222.2861-3.10713.18985.0888-3.93054.3954-0.27620.0486-0.10480.12460.2848-0.29-0.4657-0.01360.09290.4511-0.0034-0.03550.2906-0.01010.322124.776837.9559-58.6971
236.88231.28212.84745.12810.98093.4277-0.04190.1205-0.0831-0.289-0.03660.4741-0.1495-0.30340.10830.3430.03750.01340.238-0.01120.3018.169731.3281-70.9434
247.2876-0.9014-0.08112.73970.00923.21020.0394-0.32220.24330.2962-0.20850.8298-0.324-0.94720.14960.4870.00790.10820.5368-0.1120.47931.944430.0596-64.3405
252.0543.97684.38712.0716.88.152-0.23360.3659-0.2301-0.10320.0162-0.6571-0.21190.23690.21350.56-0.0855-0.00510.29080.02050.359725.624532.6477-64.5769
264.91171.11281.32997.68191.8542.9427-0.2585-0.13320.3557-0.2724-0.30241.4074-0.3385-0.69450.51110.45810.1118-0.03750.4632-0.10270.49661.941134.5946-70.7519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )H0
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 75 )H0
3X-RAY DIFFRACTION3chain 'H' and (resid 76 through 87 )H0
4X-RAY DIFFRACTION4chain 'H' and (resid 88 through 111 )H0
5X-RAY DIFFRACTION5chain 'H' and (resid 112 through 213 )H0
6X-RAY DIFFRACTION6chain 'L' and (resid 2 through 18 )L0
7X-RAY DIFFRACTION7chain 'L' and (resid 19 through 38 )L0
8X-RAY DIFFRACTION8chain 'L' and (resid 39 through 75 )L0
9X-RAY DIFFRACTION9chain 'L' and (resid 76 through 101 )L0
10X-RAY DIFFRACTION10chain 'L' and (resid 102 through 115 )L0
11X-RAY DIFFRACTION11chain 'L' and (resid 116 through 130 )L0
12X-RAY DIFFRACTION12chain 'L' and (resid 131 through 165 )L0
13X-RAY DIFFRACTION13chain 'L' and (resid 166 through 213 )L0
14X-RAY DIFFRACTION14chain 'A' and (resid 1 through 33 )A0
15X-RAY DIFFRACTION15chain 'A' and (resid 34 through 66 )A0
16X-RAY DIFFRACTION16chain 'A' and (resid 67 through 119 )A0
17X-RAY DIFFRACTION17chain 'A' and (resid 120 through 213 )A0
18X-RAY DIFFRACTION18chain 'B' and (resid 2 through 18 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 19 through 48 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 49 through 75 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 76 through 102 )B0
22X-RAY DIFFRACTION22chain 'B' and (resid 103 through 115 )B0
23X-RAY DIFFRACTION23chain 'B' and (resid 116 through 152 )B0
24X-RAY DIFFRACTION24chain 'B' and (resid 153 through 165 )B0
25X-RAY DIFFRACTION25chain 'B' and (resid 166 through 176 )B0
26X-RAY DIFFRACTION26chain 'B' and (resid 177 through 214 )B0

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