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- PDB-4jdv: Crystal structure of germ-line precursor of NIH45-46 Fab -

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Basic information

Entry
Database: PDB / ID: 4jdv
TitleCrystal structure of germ-line precursor of NIH45-46 Fab
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / IG FOLD / ANTI HIV ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsDiskin, R. / Scharf, L. / Bjorkman, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for HIV-1 gp120 recognition by a germ-line version of a broadly neutralizing antibody.
Authors: Scharf, L. / West, A.P. / Gao, H. / Lee, T. / Scheid, J.F. / Nussenzweig, M.C. / Bjorkman, P.J. / Diskin, R.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Jun 2, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: 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
A: Fab heavy chain
B: Fab light chain
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,70114
Polymers96,4114
Non-polymers1,28910
Water16,412911
1
A: Fab heavy chain
B: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8008
Polymers48,2062
Non-polymers5956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-41 kcal/mol
Surface area19650 Å2
MethodPISA
2
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9006
Polymers48,2062
Non-polymers6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-42 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.960, 70.140, 225.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 25186.221 Da / Num. of mol.: 2 / Fragment: NIH45-46 Germ-line HEAVY CHAIN, IG GAMMA-1 CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Antibody Fab light chain / Fragment antigen-binding


Mass: 23019.514 Da / Num. of mol.: 2 / Fragment: NIH45-46 Germ-line Light CHAIN, IG Kappa
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 921 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: PEG 3350, ammonium sulfate, Bis-Tris , pH 5.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2012
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4878→39.6828 Å / Num. obs: 140662 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.142
Reflection shellResolution: 1.65→1.78 Å / Rmerge(I) obs: 1.01 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å39.68 Å
Translation2.8 Å39.68 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7W

3u7w


Resolution: 1.65→37.888 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.8742 / SU ML: 0.13 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 1826 1.71 %RANDOM
Rwork0.1738 ---
obs0.1744 106921 99.38 %-
all-107588 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.88 Å2 / Biso mean: 25.5521 Å2 / Biso min: 7.09 Å2
Refinement stepCycle: LAST / Resolution: 1.65→37.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 80 911 7597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086862
X-RAY DIFFRACTIONf_angle_d1.1849306
X-RAY DIFFRACTIONf_chiral_restr0.0761021
X-RAY DIFFRACTIONf_plane_restr0.0061181
X-RAY DIFFRACTIONf_dihedral_angle_d13.7852478
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69460.2591380.21768010814899
1.6946-1.74450.25141390.20777940807999
1.7445-1.80080.23711380.19747978811699
1.8008-1.86510.23451390.190180028141100
1.8651-1.93980.25171390.185180038142100
1.9398-2.02810.25481390.182880028141100
2.0281-2.1350.18251400.17918035817599
2.135-2.26880.20821400.174880738213100
2.2688-2.44390.19491410.173681108251100
2.4439-2.68980.21441410.17481158256100
2.6898-3.07890.19691420.17228131827399
3.0789-3.87840.18691430.152482428385100
3.8784-37.89820.17861470.17078454860198
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)
10.909-0.00110.20970.9337-0.21821.93030.016-0.0429-0.0886-0.0335-0.01410.04850.1352-0.01910.01450.09990.0067-0.00230.11980.00410.143620.063412.181132.2555
20.8514-0.12280.34710.914-0.06770.90510.03560.00660.0378-0.0431-0.0123-0.0645-0.1195-0.0648-0.02280.13050.0078-0.00710.11650.00690.147419.890322.345125.2908
30.8457-0.10830.37450.211-0.28340.89770.02250.01720.0084-0.04230.0071-0.0022-0.0606-0.023-0.02840.08340.00220.00880.0680.00130.082315.980720.126925.555
40.0909-0.11420.26180.7511-0.17341.29260.1996-0.2734-0.18740.2764-0.2401-0.01810.05090.06170.07930.15710.00910.01680.32750.03890.19311.92173.023354.263
51.42370.8970.23121.0479-0.29291.11580.0558-0.1846-0.1261-0.0829-0.1336-0.02210.14870.12670.09590.14460.02410.00960.2286-0.00310.1888-1.90611.622447.5258
65.79061.8896-2.90992.0682-1.58883.057-0.0354-0.6138-0.22660.0631-0.13010.07490.39060.15940.01620.27930.02290.00150.34420.08350.3498-4.0569-7.216455.4692
71.44660.33150.11861.59470.19951.82960.0446-0.18240.24580.1250.02640.1533-0.1463-0.1469-0.07060.15510.02650.00320.1520.00620.195-8.040727.346827.9621
81.7015-0.3276-0.03621.3647-0.12441.56720.0304-0.01360.3146-0.09240.0039-0.0332-0.35680.0138-0.01810.21990.005-0.00020.16690.01420.21941.082631.815621.4588
91.19740.5809-0.97452.6542-2.42482.55810.1143-0.0426-0.5045-0.21850.12330.23080.4881-0.031-0.07150.17850.0089-0.00540.18680.02710.18921.954915.376424.4611
102.10291.0066-0.25230.9386-0.73431.5672-0.03270.2568-0.0469-0.10990.0157-0.0419-0.1533-0.1481-0.02620.16120.0076-0.01550.21010.02970.2038-2.411626.133914.928
112.88290.8395-0.22580.6717-0.26960.955-0.02440.0248-0.0307-0.04230.06590.0402-0.0715-0.0709-0.02760.14780.01050.00160.13650.01370.1525-1.220923.638424.3304
122.81261.8172-2.58981.1258-1.72482.30950.05420.20310.25770.02080.11340.0689-0.074-0.2852-0.06040.12760.0101-0.01130.21160.03770.1649-15.44918.214134.1529
131.0733-0.17760.24420.9306-0.34442.1641-0.0228-0.04820.0240.0027-0.069-0.0670.040.26210.08320.1299-0.0049-0.0070.20660.01170.1522-8.813410.588754.6745
140.4283-0.2877-0.7850.17610.221.83030.0358-0.00560.1454-0.04590.00150.0384-0.21960.18640.00520.1967-0.0403-0.00860.1938-0.01340.1818-6.719619.106959.8685
150.62250.0621-0.04620.5255-0.55352.4072-0.0522-0.03990.0640.0357-0.0421-0.0036-0.04360.2860.0750.1286-0.0056-0.00930.1721-0.00320.1508-8.398812.061654.6593
161.3158-0.06090.01710.7018-0.16042.2997-0.05930.00070.13510.0628-0.0354-0.0261-0.0893-0.2673-0.00610.14150.0112-0.00690.1718-0.01510.1509-18.388813.630556.9393
170.5392-0.2319-0.52761.3932-0.50381.47050.06580.0415-0.0627-0.1682-0.1109-0.11390.1330.15790.01270.18560.0339-0.00520.13420.01050.169-22.2521-30.125832.1685
181.1426-0.4398-0.631.4151-0.31691.30110.06670.00110.0197-0.0997-0.0672-0.11440.07260.1283-0.01260.17970.0183-0.00790.13020.01980.1561-23.7037-26.19933.2554
191.3640.437-0.31230.55290.11370.7185-0.1306-0.43220.08790.39450.0569-0.06820.29670.45560.0890.41260.13980.0620.319-0.02570.2917-4.4495-15.91585.7429
201.3676-1.1163-0.97240.98430.19221.6797-0.2432-0.3580.08550.2880.2083-0.25640.46130.5420.05620.31620.1356-0.02810.3335-0.02120.2496-5.4687-10.705411.8719
211.21040.0004-0.43792.76340.86281.7735-0.1811-0.13720.22910.40240.5033-0.4790.22990.5849-0.0910.27110.1044-0.0660.3726-0.10360.3745-0.1298-5.864110.796
220.9998-0.27760.58518.0681-2.8651.7354-0.10920.3951-0.32170.3570.105-0.94410.58570.94220.01870.38970.1922-0.02140.5319-0.16230.53265.487-11.95458.1067
230.79420.58770.10310.8751-0.05791.1798-0.01710.0404-0.0642-0.19870.13520.10840.124-0.1119-0.10410.1899-0.0114-0.0340.13990.02580.1794-32.2286-4.248227.7717
241.48721.054-0.52581.7428-0.46670.3369-0.08730.10310.1005-0.20620.10880.05520.0604-0.16340.00720.1676-0.0155-0.01480.14560.00840.1496-36.5372-11.475133.9932
252.90810.3685-1.95841.3513-0.70641.63680.0864-0.33470.56730.09930.1906-0.57060.24970.6327-0.02580.1446-0.01140.03490.1708-0.00140.2819-19.847-11.875433.7313
260.62350.2371-0.20061.7894-0.03890.94790.0299-0.04410.04750.0258-0.03270.0105-0.022-0.06-0.00290.14030.0019-0.00760.13170.01110.1502-30.0612-8.02236.7568
270.91180.9867-0.88091.6234-0.94230.7229-0.020.0551-0.01-0.04090.0348-0.04580.0373-0.0515-0.03280.16440.0060.01440.14180.01220.1614-22.02084.586221.9832
281.6586-0.9279-0.15564.03811.10161.80210.07980.20940.1711-0.1310.1685-0.87890.24870.53280.00580.26750.07820.0430.2963-0.0180.2321-5.4408-6.6523-1.9365
290.5263-0.2013-0.771.43511.57593.34120.01310.01860.0098-0.0120.073-0.01290.2321-0.0133-0.01770.1960.00510.0040.14740.00490.1574-17.5164-1.25855.9997
300.2532-0.260.58610.4584-0.84782.60950.09-0.028-0.1012-0.09290.15730.2870.2422-0.3298-0.08790.2499-0.0343-0.02070.20470.03030.2127-20.7466-7.3126-1.871
311.803-0.2611-0.06334.15221.11863.184-0.2525-0.38580.09550.37950.4416-0.50310.42630.5938-0.07980.1920.0569-0.00120.2259-0.0260.1846-14.18641.401120.7903
321.0954-0.3183-0.13771.16830.16161.71240.07340.3231-0.1094-0.2112-0.1145-0.05230.3408-0.16530.040.28610.0369-0.00570.2445-0.01230.1693-14.1522-7.1348-5.9117
331.20860.0298-0.01321.3290.05442.07780.11510.2423-0.1293-0.3617-0.2350.0927-0.6203-0.016-0.06230.22140.0302-0.00950.1890.02990.1759-16.65545.028-0.9004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 75 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 115 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 138 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 207 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 224 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 18 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 38 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 48 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 75 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 76 through 97 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 98 through 109 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 110 through 146 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 147 through 159 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 160 through 193 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 194 through 209 )B0
17X-RAY DIFFRACTION17chain 'H' and (resid 2 through 75 )H0
18X-RAY DIFFRACTION18chain 'H' and (resid 76 through 115 )H0
19X-RAY DIFFRACTION19chain 'H' and (resid 116 through 139 )H0
20X-RAY DIFFRACTION20chain 'H' and (resid 140 through 179 )H0
21X-RAY DIFFRACTION21chain 'H' and (resid 180 through 207 )H0
22X-RAY DIFFRACTION22chain 'H' and (resid 208 through 217 )H0
23X-RAY DIFFRACTION23chain 'L' and (resid 1 through 18 )L0
24X-RAY DIFFRACTION24chain 'L' and (resid 19 through 38 )L0
25X-RAY DIFFRACTION25chain 'L' and (resid 39 through 48 )L0
26X-RAY DIFFRACTION26chain 'L' and (resid 49 through 97 )L0
27X-RAY DIFFRACTION27chain 'L' and (resid 98 through 109 )L0
28X-RAY DIFFRACTION28chain 'L' and (resid 110 through 124 )L0
29X-RAY DIFFRACTION29chain 'L' and (resid 125 through 146 )L0
30X-RAY DIFFRACTION30chain 'L' and (resid 147 through 159 )L0
31X-RAY DIFFRACTION31chain 'L' and (resid 160 through 170 )L0
32X-RAY DIFFRACTION32chain 'L' and (resid 171 through 193 )L0
33X-RAY DIFFRACTION33chain 'L' and (resid 194 through 209 )L0

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