Supporting Information Guan et al. 10.1073/pnas.1217609110 Fig. S1. Three patterns of reactivity for CD4-induced (CD4i) mabs. The following representative ELISAs show three patterns of reactivity for CD4i mabs. Note that none of the mabs bind trimeric HIV-1 envelope glycoprotein (Env), SOSIP. ELISAs were carried out as described in Materials and Methods for the mabs listed in Table 1. Pattern 1: mabs that exhibit 10- to 30-fold preferences for binding gp120-cd4 complexes over monomeric gp120. mab N12-i3 is the example. The following mabs from Table 1 exhibit this pattern: cluster A, L9-i1 and N12-i3; unassigned, N10-i6.1. Pattern 2: mabs that exhibit >30-fold preferences for binding of gp120-cd4 complexes over monomeric gp120. mab N12-i2 is the example. The following mabs from Table 1 exhibit this pattern: cluster A, N5-i5 and L9-i2; cluster C.1, N5-i1, N5-i3, N5-i4, N10-i1.1, N10-i5.3, N12-i1, N12-i2, N12-i4, N12-i5, N12-i7, N12-i8, and L9-i3; cluster C.2, N12-i10, N12-i17, N12-i18, and N12-i19; cluster C.3, N5-i2, N5-i6, N5-i14, N5-i7, N5-i12, N10-i3.1, and N12-i12; cluster C.4, N12-i14 and N5-i13; unassigned, N10-i4. Pattern 3: mabs that are strictly specific for gp120-cd4 complexes. mab N12-i15 is the example. The following mabs from Table 1 exhibit this pattern: cluster A, N26-i1; cluster B, N12-i15; cluster C.1, N5-i8; cluster C.3, N5-i9, N12-i9, and N12-i11; cluster C.4, L9-i4, N5-i10, N10-i2, and N12-i16. Fig. S2. Epitope mapping of the cluster B mab N12-i15. (A) mab competition ELISA using a limiting concentration of biotinylated N12-i15 and known CD4i mabs recognizing coreceptor binding site (CoRBS) epitopes 17b, 48d, E51, 412d, and IgGm9 (X5 derivative)] or a cluster A epitope, A32. (B) Deletion mutant mapping for N12-i15 by ELISA using full-length single-chain gp120-cd4 monomer (FLSC), FLSC-ΔV3, FLSC-ΔV1/ΔV2, or FLSC-ΔV3, ΔV1/ΔV2/ΔV3 and control mabs 17b (CoRBS) or b12 (CD4-binding site, CD4bs). (C) The I420R mutation in gp120 alters binding of N12-i15 to gp120-cd4 complexes. mabs 17b (CoRBS specific) and N12-03.1 (V3 specific) were used as positive controls. 1of6
Fig. S3. Stereo view of superimposed symmetry-related antigen-binding fragment (Fab) molecules present in the asymmetric unit of crystals of Fab A32, Fab N5-i5, and Fab N12-i15. Cα traces are shown as ribbons. A32: Fab A32 crystallized in the triclinic space group P1 with two Fabs (referred as Fab and Fab2 )in the asymmetric unit. Residue segment SKS 130H of the heavy chain constant region (C H ) of Fab1 and GGSSSS H31 of the variable heavy chain (V H ) of Fab2 were poorly accountable in the electron densities and were omitted in the final model. Two structurally independent Fab A32 molecules are highly similar, with an rmsd of Cα superimposition for the entire molecule of 0.82 Å and the variable (V) region of 0.75 Å. N5-i5: Fab N5-i5 formed crystals in monoclinic space group P2 1 which contained four Fabs in the asymmetric unit. The densities of each of four copies were very well defined with one residue segment of the C H (residues SSKSTSGG H134 ) missing in each copy and omitted in the final refinement. Pairwise superposition of Fab molecules present in the asymmetric unit of crystal yielded Cα rmds values for all atoms ranging between 0.51 and 1.10 Å and a V domain of 0.21 0.31 Å. N12-i15: Crystals of Fab N12-i15 were indexed in space group P4 3 and contained four Fab molecules per asymmetric unit. Three Fab molecules were well defined with few residue segments of the constant regions disordered and excluded from the final model (SSKSTSGG H134 of Fab1, Fab2 and Fab3; residues GTQ H191 of Fab2 and Fab3; and residues KVD L150 of Fab3). In contrast, entire constant region of the fourth Fab molecule was insufficiently ordered, with several residues characterized by poorly defined electron density. These residues were omitted in building the final model. Pairwise superposition of Fab molecules present in the asymmetric unit of crystal N12-i15 yielded Cα rmds values for all atoms in a range of 0.34 1.0 Å and a V domain of 0.23 0.35 Å. N12-i2: The hexagonal crystals of Fab N12-i2 were indexed in space group Legend continued on following page 2of6
P6 1 22 and contained one Fab molecule per asymmetric unit (not shown). Residues SYYEPGTSYH 100h of the complementarity-determining region (CDR) H3 loop and residues SSKSTSGG H134 and G H157 of the C H region were disordered and therefore were excluded from the final model. In addition some solvent-exposed regions of the C H and light change constant region (C L ) were weakly ordered as indicated by poorly defined electron density. Fig. S4. Tyrosine sulfation of N12-i2 CDR H3 C 4 reversed-phase (RP)-HPLC and electrospray ionization mass spectrometry (ESI-MS) analysis of purified N12-i2 Fab. Protein was analyzed on a Symmetry 300 C 4 column (2.1 150 mm, 3.5 μm) using a linear gradient of 5 65% of acetonitrile at a flow rate of 0.25 ml/min over 30 min. Deconvoluted ESI mass spectra are shown for a C 4 RP-HPLC elution peak. ESI-MS identified three protein components with masses corresponding to nonsulfated (49,014 Da), singly sulfated (49,096 Da) and doubly sulfated (49,173 Da) Fab N12-i2. Determined molecular masses are in agreement with expected values calculated based on the average isotope compositions of the oxidized form which include four intrachain and one interchain disulfide bonds (49,013; 49,094, and 49,174 Da, respectively). A presence of one sulfogroup corresponds to a +80 change in mass. 3of6
Table S1. Neutralization by CD4i mabs IC 50 titer in TZM-bl cells (ug/ml) Tier 1 Clade B Tier 1 Clade A Tier 1 Clade C Tier 2 Clade B Negative control Epitope cluster mab SF162 BaL.26 SS1196.1 DJ263.8 MS208.A1 MW965.26 TV1.1 6535.3 QH0692.42 THRO4156.18 REJO4541.58 WITO4160.33 MuLV HIV2+sCD4 Cluster A L9-i1 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N5-i5 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 L9-i2 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N12-i3 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N26-i1 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 Cluster B N12-i15 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 Cluster C.1 N5-i1 1.1 >50 13.8 >50 >50 0.9 >50 >50 3.9 >50 >50 >50 >50 >50 N5-i3 1 21.7 5.3 >50 >50 0.9 >50 >50 >50 >50 >50 >50 >50 >50 N5-i4 1.4 44 15.5 >50 >50 0.3 >50 >50 4.2 >50 >50 >50 >50 >50 N10-i1.1 0.86 10.5 10.9 >50 >50 9.5 >50 >50 >50 >50 >50 >50 >50 >50 N10-i5.3 3.2 29.1 10 44.7 >50 0.07 >50 >50 35.8 >50 >50 >50 >50 >50 N12-i1 1.8 40.2 16.9 47.7 >50 0.2 >50 >50 5.8 >50 >50 >50 >50 >50 N12-i2 1 11.6 8.9 >50 >50 0.08 >50 >50 5 >50 >50 >50 >50 9 N12-i4 1.7 38.7 40.3 >50 >50 7.3 >50 >50 21.3 >50 >50 >50 >50 <0.1 N12-i5 3.8 >50 39.6 >50 >50 0.2 >50 >50 >50 >50 >50 >50 >50 >50 N12-i7 1.6 32.1 32.1 >50 >50 1.1 >50 >50 17.8 >50 >50 >50 >50 >50 N12-i8 3.1 >50 39.4 >50 >50 0.5 >50 >50 >50 >50 >50 >50 >50 >50 L9-i3 1.7 30.1 15.5 >50 >50 >50 >50 >50 3 20.2 >50 >50 >50 >50 N5-i8 2.6 31.6 22.4 >50 >50 0.2 >50 >50 >50 >50 >50 >50 >50 >50 Cluster C.2 N12-i10 7.3 >50 >50 >50 >50 3.1 >50 ND ND ND ND >50 >50 >50 N12-i17 3.5 41.4 25.3 >50 >50 0.1 >50 >50 >50 >50 >50 >50 >50 >50 N12-i18 2.4 >50 40.8 >50 >50 0.3 >50 >50 9.2 >50 >50 >50 >50 >50 N12-i19 2.3 >50 41.1 >50 >50 0.3 >50 >50 20.5 >50 >50 >50 >50 >50 Cluster C.3 N5-i2 27.7 >50 >50 >50 >50 9.3 >50 >50 >50 >50 >50 >50 >50 >50 N5-i6 3.2 46 24.2 >50 >50 13.4 >50 >50 >50 >50 >50 >50 >50 >50 N5-i14 5.3 >50 27.8 >50 >50 0.6 >50 >50 >50 >50 >50 >50 >50 >50 N5-i7 4.2 >50 19.3 >50 >50 0.5 >50 >50 >50 >50 >50 >50 >50 >50 N5-i12 42.2 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N10-i3.1 3.1 34.9 22.4 >50 >50 0.08 >50 >50 >50 >50 >50 >50 >50 >50 N12-i12 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N5-i9 3.9 48.8 22.3 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N12-i9 3.2 46.6 >50 >50 >50 9.5 >50 >50 >50 >50 >50 >50 >50 >50 N12-i11 36.1 >50 >50 >50 >50 49.4 >50 >50 >50 >50 >50 >50 >50 >50 Cluster C.4 L9-i4 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N12-i14 1.3 38.8 20 >50 >50 >50 >50 >50 13.8 >50 >50 >50 >50 >50 N5-i10.1 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N10-i2 12.7 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N5-i13 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N12-i16 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 Unassigned N10-i4 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 N10-i6.1 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 4of6
Table S1. Cont. IC 50 titer in TZM-bl cells (ug/ml) Tier 1 Clade B Tier 1 Clade A Tier 1 Clade C Tier 2 Clade B Negative control Epitope cluster mab SF162 BaL.26 SS1196.1 DJ263.8 MS208.A1 MW965.26 TV1.1 6535.3 QH0692.42 THRO4156.18 REJO4541.58 WITO4160.33 MuLV HIV2+sCD4 Controls C11 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 A32 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 17b 8.5 39.8 26.9 >50 >50 0.3 >50 >50 6.2 >50 >50 >50 >50 <0.1 19e >5 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 >50 <0.1 b12 0.09 0.07 1.9 >50 0.7 <0.02 >50 7.3 0.3 2.5 6.4 25.1 >50 >50 Neutralization was carried out as described in Materials and Methods using HIV-1 or HIV-2 pseudoviruses. ND, not done. 5of6
Table S2. Data collection and refinement statistics Crystal A32 Fab N5-i5 Fab N12-i15 Fab N12-i2 Fab Data collection Wavelength ( Å) 1.00 1.00 0.98 0.98 Space group P1 P2 1 P4 3 P6 1 22 Cell parameters a, b, c (Å) 40.8, 71.3, 77.7 73.4, 84.5, 143.1 125.1, 125.1, 149.9 78.9, 78.9, 315.2 α, β, γ ( ) 103.7, 104.0, 105.4 90, 101, 90 90, 90, 90 90, 90, 120 Molecules (a.u.) 2 4 4 1 Resolution (Å) 50 1.85 (1.88 1.85) 50 1.95 (1.98 1.95) 50 2.59 (2.68 2.59) 50 1.95 (2.02 1.95) Number of reflections Total 117,353 232,588 256,664 200,085 Unique 59,060 123,808 71,607 43,782 R merg (%)* 12.0 (90.3) 11.3 (76.5) 14.5 (78.3) 9.4 (79.5) I/σ 17.9 (1.5) 12.7 (2.0) 16.3 (2.7) 54.6 (2.5) Completeness (%) 90.0 (89.5) 98.5 (98.7) 100.0 (99.9) 99.9 (99.7) Redundancy 3.8 (3.6) 3.5 (3.4) 20.2 (15.2) 7.6 (7.5) Refinement statistics Resolution, Å 36 1.85 20 1.95 20 2.6 20 1.95 R(%) 18.7 19.8 21.6 20.3 R free (%) 23.2 24.5 25.4 23.6 Number of atoms Protein 6,454 13,436 12,840 3,265 Water 355 802 566 298 Ligand/Ion 7 62 49 0 Overall B value (Å 2 ) Variable domain 37.1 36.0 33.0 38.4 Constant domain 36.5 40.7 40.6 46.3 Water 29.6 40.2 37.5 41.3 rmsd Bond lengths (Å) 0.017 0.019 0.019 0.020 Bond angles ( ) 1.5 1.7 1.8 1.8 Ramachandran Favored (%) 95.5 96.8 95.5 97.4 Allowed (%) 4.3 3.0 3.9 2.4 Outliers (%) 0.2 0.2 0.6 0.2 Protein Data Bank code 3TNM 3TNN 3QEH 3QEG All data outer shell. Values in parentheses are for highest-resolution shell. a.u., arbitrary units. *Rmerge = I - <I> / I, where I is the observed intensity and <I> is the average intensity obtained from multiple observations of symmetry-related reflections after rejections. R = F o - F c / F o, where F o and F c are the observed and calculated structure factors, respectively. R free defined by Brünger (1). Calculated with MolProbity (2). 1. Brunger AT (1992) Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355(6359):472 475. 2. Chen VB, et al. (2010) MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(Pt 1):12 21. Table S3. Crystallization conditions Fab A32 N5-i5 N12-i15 N12-i2 Protein concentration Crystallization conditions 12 mg/ml 10 mg/ml 8 mg/ml 10 mg/ml 20% PEG 4000, 0.1 M Hepes, ph 7.5, 10% 2-propanol 30% PEG 4000, 0.2 M ammonium sulfate 2.2% PEG 400, 2 M ammonium sulfate, 0.1 M Hepes, 0.2 ph 7.5 20% wt/vol PEG 2,000, monomethyl ether. 0.01 M nickel (II) chloride hexahydrate, 0.1 M Tris HCl, 0.02 ph 8.5 6of6